Showing posts with label Rumi. Show all posts
Showing posts with label Rumi. Show all posts

2019/03/08

(5) Ok-kyung Pak - Inter-cultural trip to Turkey

(5) Ok-kyung Pak - Inter-cultural trip to Turkey Un cadeau tombé du...



Inter-cultural trip to Turkey
Un cadeau tombé du ciel : Inter-cultural trip to Turkey (2011)
Ok-Kyung Pak 2011-08-16, Montrea
Introduction
Have you ever heard of the Intercultural Dialogue Institute (IDI) in Canada and intercultural trips to Turkey sponsored by it? No. It is not a travel agency. It is an NGO (www.interculturaldialog.ca), located in 9 cities of Canada with headquarters in Toronto. I heard about it in the spring of 2011 from a friend and I grabbed the opportunity for the trip, scheduled for July (1-11). I just completed the trip.
I know life is not fair, yet in everyone's life, some rare opportunities are presented. Knowingly or unknowingly, one has to recognize these opportunities presented to oneself, and make the best of them. My contact with IDI and the trip to Turkey is one of those opportunities, as I realize now when I am writing this essay. This contact was through a friend. You might say it was an accident, but I would say that my friend is one of many angels who have helped me throughout my life so far, since she brought me this unique opportunity for a new opening/direction, when I am starting a new phase of my life – retirement. Life has interesting twists, and there are many angels,when one cares to see them.
How could I have guessed that this trip was a preparation, mediated by a Catholic French woman, to allow a pilgrimage in an Islamic country for a Korean- Canadian Buddhist anthropologist in retirement, still looking for a spiritual Eldorado in this world? I have been preparing myself looking for a vocation to make the best use of the last segment of my life- search for a spiritual Eldorado, which is described in my short autobiography - a contribution to my mother's biography (published in Korea, 2010). Opinions are divided in different religious traditions on whether there is such a place as a spiritual Eldorado in this world. I would like to say that we have no choice but to construct one even if there is none, since we brought our children to this world .
A passage in the Bible justifies my search for Eldorado in this world as below: « And on this rock I will build my church, and the gates of Hades will not
overcome it. I will give you the keys of the kingdom of heaven; whatever you bind on earth will be bound in heaven. And whatever you lose on earth will be lost in heaven » (Matthew 16:18-19).
Apparently, this passage inspired the construction of the first church carved in the rock of Antakya that spread Christianity in Cappadocia. (Cappadocia, by Jeoffrey Larmec, 2010) (see below for more on Cappadocia)
Trip in Turkey
The most fascinating aspect of Turkey for me was that it is the land of a meeting point of the West and the East. I heard about this characteristic of Turkey, but until I landed there, I did not exactly understand what it meant. I would strongly recommend that one should visit China to understand the civiliziation of the East, and visit Turkey to understand the meeting of the Eastern and Western civilizations, which was then called by the name of the Ottoman Empire.
The glory of the Ottoman Empire has declined after so many centuries and now modern Turkey is blooming with much complexities and challenges. As Rumi , a mystic Sufi 'master' wrote at his time (13th century):
Il est bon de franchir chaque jour une étape
Comme l'eau vive qui ne stagne pas
Hier s'est enfui, l'histoire d'hier elle aussi est passée
Il convient aujourd'hui de conter une histoire nouvelle
(Les Quatrains de Rumi)
We visited 5 cities (Istanbul – north west; Antalya – southwest coast; Izmir – west coast; Kayseri & Konya – central Turkey) (see a map of Turkey attached, with 5 cities marked). Our group consisted of 4 people. The group was led by a charming young man, the Executive Director of IDI. His ingenuity in finding solutions to all kinds of small problems encountered during the trip as in any group travel, his spontaniety, energy, sincerity, and a total confidence in what he was doing cannot be praised enough. Nobody can do such a job without a conviction. It was delightful to be led by him.
As for the organization of the trip, there is room for some improvement. No explanation was offered why these cities were chosen for our trip, nor the schedule of the trip, until half way through our trip. Different groups seem to have visited other cities, overlapping with some we visited. However, in retrospect our itinerary made sense, since each of these cities allowed us to see and taste , within a limited time, different geographical features , different cultures, religions and civilizations that inhabited this vast land. I have been always attracted to Turkey, but most of all Istanbul, since Turkey was for me synonymous with Istanbul., an ancient, cosmopolitan city from the period when it was called Constantinople. The rest of Turkey did not mean much to me. Now I became aware of my profound ignorance of this country, the region and its history. Since I came back from the trip, I
have been complementing my knowledge on Turkey, by reading history books, novels and tourism books. It is simply fascinating.
Some of the places and historical sites we visited
We arrived in Istanbul on Friday night. Immediately early next morning we flew to Antalay - a southern coastal city.
Antalay:
This is a resort area for the Turks as well as people from the region. This visit allowed us to start our trip in a real holiday mood. We spent the entire weekend there. The hotel was very comfortable, the sea beautiful. Our charming guide - executive director of the IDI contacted his uncle who has a small family run tourist business on the beach. Luckily, he did not have any reservation of his boat by tourists, and offered us a motor boat excursion along the coast. It was an imemorable afternoon. The boat was equipped with a mongolfare, and when the motor speeded up, the mongolfare attached to the boat flew high in the blue sky. Some of us adventured to fly on it. We even swam for 10 minutes in the beautiful, immense blue Meditarenean sea. We were small dots in the immense space of the blue sea simmlessly connected by the blue sky.
Ephesus in the City of Izmir:
From Antaly we flew to Izmir, which is in the western part of Anatolia, to see the
ruins of Ephesus from Roman era. Ephesus is near the historical town of Seljuk, between the cities of Aydin and Izmir.
As one enters the ruins, it is not difficult to imagine the historical past of the city- that of the Roman era, when Ephesus was the capital of five hundred Anatolian towns. This was after the period in which Homer wrote his immortal works, but coincides with the time in which St. John lived and died. Two important figures in Christian religion – St. Paul and St. John lived in Ephesus, attracting the interest of Christians all over the world even now.
The glory of Ephesus at its height is described by Naci Keskin (Ephesus, 2011) as below:
« At that time you could see the stairs of the colossal theatre from the sea far away, and the huge gleaming columns of the temple of Artemis, which once used to blind people with their beauty. About 250,000 people used to live in this famous city where the most skilful artisans and rich merchants gathered together. ....Sportmen, musicians and theatre players used to attract people from the surrounding area, and apectators from as far away as Jerusalem and Athens as well....The ruins of Ephesus are magnificent. Though hundreds of years have passed, and in spite of the ravages of time, they have survived to the present day, and they still preserve their grace and elegance. (p.3).
The Cappadocia region-another planet:
From Izmir, we flew to Kayseri in central Turkey. Göreme is situated between the cities of Kayseri and Nevsehir. This area is the Cappadocia region. The alttitude of Nevsehir is between 500-1000m, and most of the geologial and historical wonders that we saw in this area, such as unique valleys, elongated mushroom shape fairy chimneys, rock dwelling churches, underground cities, and open air museums are near this city. The region looks more as though it belongs to a different planet other than Earth.
Jeffrey Lamec's description of the pre-historic state of this region helps to evoke the geological formation and scenery of Kayseri and its surroundings with volcanic layers, rock canyons and underground cities, which are completely different from other cities we saw earlier. Lamec writes (Cappadoccia, 2010: 3-5):
« Millions of years ago, during the 3rd geological period, Mid-Anatolian Plateau was an inner sea surrounded by forests and plains, which were not higher than 500 meters. In the south, between Lycaonai (northeast of Konya) and the Taurus
Mountains range, a series of volcanoes appeared as a result of the movement of the Taurus Mountains. The continuous eruptions of the mountains in this area have structured Mid-Anatolian Plateau with masses of lava and ash that are 200 meters in height. In the 4th geological era (two million years ago), the earth went through climatic changes that included four different ice ages. It is believed that the long- lasting presence of glaciers from the ice age in Asia Minor is the reason why civilizations did not inhabit this region. With the end of the ice ages climate
became milder and in Cappadocia, especially around Konya and Aksaray, several
lakes appeared. Ash, sandstone, clay, basalt and ignimbrite, soft tufa and other
minerals that make up the volcanic layers eroded by natural forces and formed the unique rock formations that are only seen in Cappadocia. Soft tufa stones and
layers were affected differently by the erosion process. .....
During the times of the Roman Empire, the people of Cappadocia chiseled rocks in order to create hiding places from the Roman tax collectors. During the reign of Emperor Septimus Severus (born in Kayseri today) economical revival occurred. Christians of Anatolia built monasteries and churches out of sight in Ihlara and
Gôreme in 4th Century by making use of the soft tufa rocks. During this time,
Aksaray and Kayseri turned into important religious centers. »
Göreme valley and the rock churches, now called Open Air Museum of Göreme,
was one of the significant centres in early Byzantine times. Towards the 11th century, a total aristocratic period began in church art. The paintings in this period, done by accompolished artists working for the emperor, are very different from the early Byzantine era. The fresco paintings on walls and ceilings of rock churches we saw were most interesting. We visited one of these rock churches – St. Barbara Church.
basalt
Underground cities of Cappadocia
These underground cities were most fascinating. Some places were so low and narrow that one has to bend 90 degrees to pass through the tunnel. It reminded me of tunnels I saw in Vietnam, built by the Vietcongs near Saigon, during the Vietnam war in order to resist the American soldiers.
The Cappadocia region was occupied by different cultures in the course of its history. People who normally dwell in houses would move into these underground caves with their domestic animals for security purposes. There are apparently a total of 200 dwellings that are known in the area. Common characteristics of the underground cities are long stables on the first floor, where all the animals were kept; long carved chimneys for air conditioning and communication between dwellings; dining room, bedrooms, kitchen with stone stoves, chapels and wineries; as well as toilets and septic wells. We visited one of these underground cities.
The Silk Road and carawanserais:
We drove from Kayseri towards Konya on what used to be called the 'Silk Road'. On the way we stopped at a carasanserai and attended a Whirling Dervish Dance Ceremony. It was most fascinating to see an elaborately decorated, imposing stone building in the middle of nowhere.
All of us heard and read about the silk road in our history book. The transportation of silk and spice, as well as other products of the east, in caravans to the west created the famous silk Road trade ways that extended from China to Europe. The Silk Road crossed Anatolia from one side to the other. It not only provided a means to transport commercial goods and people, but also the opportunity for the exchange of culture between the east and the west. During the Seljuks' rule, there were three key elements of trade: roads, caravans, and caravanserais. They symbolyzed the guarantee of the state over the commercial transportation with their castle-like appearances, decorated with rich stone ornaments and well- planned interior designs. There were rooms around the courtyard that were used as bedrooms, kitchens, baths, storage rooms, and toilets. Aside from securing the transporation of goods and travelers, they also created a channel of communication between cultures. Research shows that there were nearly 200 caravanserais in Anatolia. They were built 30-40 km from each other. We visited one of these caravanserais – Saruhan and attended a solumn Semâ ceremony.
The Semâ (whirlying Dervish dance) ceremony at Saruhan
I have always dreamed of seeing « whirling dervish dance », of which I have read about in Rumi's writing. This dream came along. It was a solemn, elegant ceremony, full of symboilism and meaning. It is said that « The Semâ ceremony
represents a mystical journey of man's spiritual ascent through love, deserts his ego, finds the truth and arrives to the ' perfect' ». In addition to the whirlying dance we saw, our visit to Saruhan presented to me another quite unexpected reflection. When we bought our tickets for the dance ceremony, we were given a leaflet. On it were a brief explanation of the dance, photos of the Dervish dancers and Rumi's seven counsels, which are:
1.In generosity and helping others, be like a river.... 2.In compassion and grace, be like the sun...
3.In concealing others' faults, be like night....
4.In anger and fury, be like the dead....
5.In modesty and humility, be like the earth... 6.In tolerance, be like a sea...
7.Either exist as you are or be as you look.
Every member of our group was very much moved by Rumi's seven counsels. Particularly the first one – be like a river in generosity and helping others- penetrated into my heart. When I read the word « river », instantly my pen name 'cloud-river' came to my mind, and I felt like I was struck by Rumi. I gave myself this name as an orientation of my life -detachment from all and everything, like cloud and river which flows without attachment. I am realizing now that the word 'river' in my name symbolizing 'detachment' reflects my profound disappointment with humanity. By detaching myself from the weakness and ugliness of humanity, I would have less disappointment and judgement of the others. On the other hand, the word 'river' in Rumi's counsel symbolizes abundance of generosity and giving to the others. The focus here is 'the other', while the river in my name focuses on myself – my disappointment with the others. The largeness of Rumi's spirit filled my heart.
Konya
Mawlana Museum (where Rumi's tomb is located) was the rose garden of the Seljuk Palace in Konya. The rose garden was still there. Apparently it was presented as a gift to Rumi's father by the Seljuk Sultan. Rumi's father was a famous scholar from what is now known as Afghanistan. He migrated to Kony escaping the invasion of Mongols in Afghanistan. Rumi's father, Rumi himself (died in 1273) and his son are buried there. The museum, displaying religious relics, was very beautiful. I was very much moved, realizing that here finally I meet Rumi, quite unexpectedly.
Istanbul
Finally we came back to Istanbul, flying from Konya. It was the last stage of our trip and we spent four days there. We visited Saint Sofia Basilique, one of the majestic remains of the Constantinople period (now called Istanbul), which was the capital of the oriental Roman Empire for almost 1000 years. Constantinople then was the richest city of Christianity. We also visited the famous blue mosque, Dolmabahçe Palace, Topkapi Palace, some of the 9 hills of the city, Spice Bazar, and crossed the famous Bosphorus by a ferry.
The time immemorial Spice Bazar was more fascinating for me than anything else, since this was and still is one of the places, where common people (not sultans) conducted their trade and wove their daily life. We visited one of the spice stores, whose owner is a member of the IDI. We were invited to come up to the upper floor of the store. This upper floor of a tiny store had a dome like ceiling painted with flowers and plants, which looked much more spacious than the actual space with its dome. With a much cooler temperature than the street, this space was like an oasis, offering a refuge from the noise and business of downstairs. After having visited majestic palaces and mosques displaying an overwhelming wealth and power of the rulers of different periods, I was relived to see and admired the ingenuity and simple aesthetics of the common people, not so wealthy as sultans. It was a breath of fresh air.
I will always remember the most delicious Turkish coffee and 'turkish delights' along with dried apricots covered with nuts offered to us at this oasis. Our mouth and eyes were filled with pleasure. Each of us was also offered with a gift of turkish delights, which delighted our hearts.
People we met and institutions visited:
We also visited a number of institutions in Istanbul, such as a TV station, a university, several high schools, an association of journalists, and a hospital. We were also invited by families in their houses for supper. These meetings at individual homes and institutions allowed us to have a glimpse of the family life in Turkey, their very strong family oriented values, their social ethos and the outlook to life of the professionals at their workplaces. Every single person we met was very clear about their life objectives and had a strong commitment to them. Their objective in life , we were told, is to bring a peace to the world and live together with others of different cultures, faiths, ethnic origins and nationalities. No wonder. It is a difficult but a noble objective in this country and region, which cradled so many different civilizations and conflicts\conquests. We were meeting members or volunteers of the IDI. These objectives are also those of IDI.
In addition to the organized meetings with people, I also met people on the street. What is most fascinating was the warm current overflowing from people on the street, when our eyes met. Some women and young girls even asked my permission to take photos of myself and also together with them. This never
happened to me (not even in my country of origin - Korea), with one exception (in Chili with an indigenous man who looked like a Korean), in all those numerous countries where I visited. I did not need Rumi's poem (see below) to feel that I came from the same origin as they.
Le coeur est un jardin secret ou se cachent des arbres
Il manifeste cent formes, mais il n'a qu'une seule forme C'est un océan immense sans limites et sans rives
Cent vagues s'y brisent, les vagues de chaque âme.
(Les Quatrins de Rumi)
Place of Gifts and food-offering in Turkey
Whenever we visited – homes or organizations- we were always offered gifts, after a meal or coffee\tea. From this pattern, we gradually learned that gifts and offers of food are very important in Turkey, and an essential part of social life. We were told to bring small gifts when we left Canada, but we were embarassed sometimes to offer such small gifts. Gifts and offers of food (meal) are an essential part of social life in Asia in general, but Turkish gifts and meals were overwhelming. We were hoping to receive a suitecase to put all of the gifts we received, but it did not happen.
Rumi's Teaching & followers: F. Gullen & IDI
Gradually, I realized that all these families we met and institutions visited are supporters\partners and volunteers of the contemporary Gullen Movement in Turkey and \or volunteers of the IDI in Canada. The core principle of the Gullen Movement is « respect for humankind ». Gullen wrote:
« Loving and respecting humanity merely because they are human is an expression of respect for the Almighty Creator. The other side of the coin, loving and showing respect to only those who think the same as one thinks, is nothing but egotism and selfworship. More than this, it is irreverent and self-conceited
behavior to hurt the feelings of others who may not think exactly as we think, but who still are on the same main road with us in their toughts and visions (more on Gullen, see James C. Harrington, Wrestling with Free Speech, Religious Freedom, and Democracy in Turkey: The Political Trials and Times of Fethullah Güllen, 2011
As I understand it, Gullen's vision arises from teachings of Jalaludin Rumi, who taught and spread a message of love transcening the boundaries of time and space. In Rumi's own words, he expressed the one origin of the humanity in his poems as below:
Je viens de cette âme qui est à l'origine de toutes les âmes
Je suis de cette ville qui est la ville de ceux qui sont sans ville
Le chemin de cette ville n'a pas de fin, Va, perds tout ce que tu as
C'est cela qui est le tout. (Les Quatrins de Rumi)
The relevance of Rumi's teaching to everybody (even non-Muslims) is pointed out by a contemporary US educated psychocologist as follows (Michaela M. Ozelsel, Rumi resonates through the Ages, pp.34-42, in Rumi & his Sufi path of love, ed. By M. Fatih Çitlak – Hüseyin Bingül, 2011):
« ...there will always be things in life that we cannot alter no matter how hard we try.... If we are Muslims, then we know: If the ego urges us to complain, do not complain; rather give thanks instead. »
But how can we convey this insight to non-Muslims? According to Ozelsel, Rumi guides the way as follows:
« This is the way of dervishes. When the mind wants to complain, do the opposite
– give thanks. Exaggerate the matter to such a degree that you find within yourself a love of what repels you. Pretending thankfulness is a way of seeking the love of God »
Epilogue:
All I saw and heard during our trip in Turkey are very familiar words and notions that I have been struggling with in my life. I never expected to meet Rumi in Turkey, since my limited knowledge of Rumi was that he was born in what is called now Afghanistan.My 10 day trip was an intense lesson on history of Turkey and the region, a re-encounter with Rumi in a completely unexpected way in a modern setting of Turkey and a re-capitulation of my life outlook/philosophy, and an opening of a new direction for the future. It turns out that my trip to Turkey was a pilgrimage to Rumi's land. I am so filled with awe and blessings I received from people I met and places I visited during my trip that I did not have to keep the carpet I bought, although I had long hoped to find such a carpet. I hope my daughter who received it as a gift receives the same blessing through the carpet coming from Turkey. END

2019/01/20

The Permaculture Handbook: Garden Farming for Town and Country: Peter Bane, David Holmgren: 9780865716667: Amazon.com: Books



The Permaculture Handbook: Garden Farming for Town and Country: Peter Bane, David Holmgren: 9780865716667: Amazon.com: Books


Permanent agriculture - abundance by design

The urban landscape has swallowed vast swaths of prime farmland across North America. Imagine how much more self-reliant our communities would be if 30 million acres of lawns were made productive again. Permaculture is a practical way to apply ecological design principles to food, housing, and energy systems; making growing fruits, vegetables and livestock easier and more sustainable.

The Permaculture Handbook is a step-by-step, beautifully illustrated guide to creating resilient and prosperous households andneighborhoods, complemented by extensive case studies of three successful farmsteads and market gardens. This comprehensive manual casts garden farming as both an economic opportunity and a strategy for living well with less money. It shows how, by mimicking the intelligence of nature and applying appropriate technologies such as solar and environmental design, permaculture can:
Create an abundance of fresh, nourishing local produce
Reduce dependence on expensive, polluting fossil fuels
Drought-proof our cities and countryside
Convert waste into wealth

Permaculture is about working with the earth and with each other to repair the damage of industrial overreach and to enrich the living world that sustains us. The Permaculture Handbook is the definitive, practical NorthAmerican guide to this revolutionary practice, and is a must-read for anyone concerned about creating food security, resilience and a legacy of abundance rather than depletion.

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Editorial Reviews

Review



Review - Transition Voice Vicki Lipski, July 26th

Peter Bane's handbook, while not quite encyclopedic, is nothing if not authoritative. I can honestly say, without fear of exaggeration, that I hold my head a little higher as I stride about my miniscule fiefdom, now that I've read The Permaculture Handbook: Garden Farming for Town and Country.
The stones Bane leaves unturned are few and far between. Once you've digested the author's ruminations on mapping, patterns, and garden elements, perennials, water, soil, plants, crops, seeds, and animal husbandry, not to mention his lists of plants and the jobs to which they are best suited, there's little chance you'll walk away dissatisfied.

Bane's treatment of these various aspects of garden farming (his preferred term) is methodical and complete. It was a relief and a delight to find that he allows both his sense of humor and political sensibilities to creep in from time to time.

He never forgets, however, that his purpose in writing is to distill over thirty years' experience in the science and the art of permaculture. There is much to be learned. The complete novice may, in fact, find the author's thoroughness a bit blinding. In this case, a piecemeal approach could well be the best one.

Bane himself advises the reader to start small, and good advice it is. As you proceed to branch out beyond the basics, the book's tidbits of information and advice will take on more and more relevance.

Pass the salt
For instance, did you know that if your fruit isn't sweet, or your vegetables are the object of an insect infestation, it's probably because your soil suffers from a mineral deficiency? Your soil is in need of amending (most everybody's is, to one degree or another).

It has been my contention, almost from the day we moved to the Cincinnati area, that the foods here are extremely bland. Now I understand why! The soil here is just awful - a tan, clumpy clay that is utterly devoid of worms and organic matter, and therefore completely unable to hold onto water. If it's possible to be deficient in everything, then this soil is. For folks in these parts, permaculture could literally spice up their lives. Good soil is the beginning of good eating.

Here's some more great advice that, by itself, is worth the purchase price of the book On page 88, we learn to,
... keep all soil growing some crop at all times
...Seed or transplant the next crop as soon as or, better, before the maturing one is harvested.

This book is packed with wisdom gleaned from decades of working the soil. Assuming I get my sonic mole repeller in time (they're tunneling me out of house and home), the winter squash will go in and around my thriving tomato plants. If I can lay my hands on some more cabbage seeds, they'll go in at the same time (the first planting was a washout).

With a cluck, cluck here...
The animal husbandry section offers a cornucopia of down-to-earth knowledge and advice.

I've long harbored the desire to raise chickens, but here - as elsewhere - we belong to a homeowners' association, so I've been frustrated yet again.
For those among you lucky enough to be able to own livestock, take a close look at chapter 14, "Animals for the Garden Farm." Interestingly, there are three animals which Bane believes the garden farmer should steer clear of: horses (not worth the upkeep), sheep (prone to parasites, need lots of land), and donkeys (need land).

He also takes on the ethical conundrum of raising animals for meat, as well as the importance of their breeding.

There is a lovely, lengthy section on beekeeping. Yet I believe this section includes a rare, important oversight; that is the failure to discuss Colony Collapse Disorder. This is just too important a problem to ignore. I hope it will be covered in the inevitable second edition.

The Permaculture Handbook is liberally adorned with black and white drawings and photographs. As can sometimes be the case with garden and farming pictures, the subjects of photos are occasionally difficult to determine. This problem is further exacerbated by the fact that permaculturists (I include myself) do not necessarily pride themselves on a tidy garden farm. Everything tends to be a "work in progress," and it shows. Such concerns notwithstanding, the color photos are particularly well done; the numbered captions are easily understood. The photos appear to have been carefully selected, and truly do add a needed dimension that bolsters the book's authoritativeness.

If they can, you can!
Finally, Bane's case studies include an up-to-the minute analysis of his own Renaissance Farm, in Bloomington, Indiana (also home to the magazine The Permaulture Activist). His year-by-year history of the progress he and partner Keith Johnson have made in turning their .7 acre into a working farm makes for genuinely interesting reading. As Bane describes the endlessly cyclical nature of what they do:
Self-reliance and food storage are both increasing. Soils are improving. The growing season is now year-round.
Would that we could all say the same.

Working examples
Other operations are described, as well: Jerome's Organics, of Basalt, Colorado; Old 99 Farm, in Dundas, Ontario; and Radical Roots Farm, of Harrisonburg, Virginia.

Jerome's is far and away the oldest of the four farms described, established in 1982. It's also different in that its primary mission is educational, both insofar as garden design is concerned, and with regard to producing successful yields. Jerome Osentowski welcomes students and visitors to his demonstration garden and educational programs year-round.

The other two garden farms were much more recently established. In the case of Old 99 Farm, operator Ian Graham sells winter vegetables, eggs, dairy and cow-shares. Radical Roots operators Dave O'Neill and wife Lee Sturgis offer annual vegetables, nursery plants, and eggs. Dave teaches permaculture design, and consults. Lee and Dave hire paid interns, affording a valuable opportunity to up-and-coming garden farmers.

I'll leave you with a parting thought of my own - this book deserves to be a part of your gardening library - and one of Peter Bane's:
The essential work of Permaculture activism is to understand and see abundance in the world around us, often before others do, and then to help others to see it also, to bring it into being.



Review - Transition Voice Vicki Lipski, July 26th

Peter Bane's handbook, while not quite encyclopedic, is nothing if not authoritative. I can honestly say, without fear of exaggeration, that I hold my head a little higher as I stride about my miniscule fiefdom, now that I've read The Permaculture Handbook: Garden Farming for Town and Country.
The stones Bane leaves unturned are few and far between. Once you've digested the author's ruminations on mapping, patterns, and garden elements, perennials, water, soil, plants, crops, seeds, and animal husbandry, not to mention his lists of plants and the jobs to which they are best suited, there's little chance you'll walk away dissatisfied.

Bane's treatment of these various aspects of garden farming (his preferred term) is methodical and complete. It was a relief and a delight to find that he allows both his sense of humor and political sensibilities to creep in from time to time.

He never forgets, however, that his purpose in writing is to distill over thirty years' experience in the science and the art of permaculture. There is much to be learned. The complete novice may, in fact, find the author's thoroughness a bit blinding. In this case, a piecemeal approach could well be the best one.

Bane himself advises the reader to start small, and good advice it is. As you proceed to branch out beyond the basics, the book's tidbits of information and advice will take on more and more relevance.

Pass the salt
For instance, did you know that if your fruit isn't sweet, or your vegetables are the object of an insect infestation, it's probably because your soil suffers from a mineral deficiency? Your soil is in need of amending (most everybody's is, to one degree or another).

It has been my contention, almost from the day we moved to the Cincinnati area, that the foods here are extremely bland. Now I understand why! The soil here is just awful - a tan, clumpy clay that is utterly devoid of worms and organic matter, and therefore completely unable to hold onto water. If it's possible to be deficient in everything, then this soil is. For folks in these parts, permaculture could literally spice up their lives. Good soil is the beginning of good eating.

Here's some more great advice that, by itself, is worth the purchase price of the book On page 88, we learn to,
... keep all soil growing some crop at all times
...Seed or transplant the next crop as soon as or, better, before the maturing one is harvested.

This book is packed with wisdom gleaned from decades of working the soil. Assuming I get my sonic mole repeller in time (they're tunneling me out of house and home), the winter squash will go in and around my thriving tomato plants. If I can lay my hands on some more cabbage seeds, they'll go in at the same time (the first planting was a washout).

With a cluck, cluck here...
The animal husbandry section offers a cornucopia of down-to-earth knowledge and advice.

I've long harbored the desire to raise chickens, but here - as elsewhere - we belong to a homeowners' association, so I've been frustrated yet again.
For those among you lucky enough to be able to own livestock, take a close look at chapter 14, "Animals for the Garden Farm." Interestingly, there are three animals which Bane believes the garden farmer should steer clear of: horses (not worth the upkeep), sheep (prone to parasites, need lots of land), and donkeys (need land).

He also takes on the ethical conundrum of raising animals for meat, as well as the importance of their breeding.

There is a lovely, lengthy section on beekeeping. Yet I believe this section includes a rare, important oversight; that is the failure to discuss Colony Collapse Disorder. This is just too important a problem to ignore. I hope it will be covered in the inevitable second edition.

The Permaculture Handbook is liberally adorned with black and white drawings and photographs. As can sometimes be the case with garden and farming pictures, the subjects of photos are occasionally difficult to determine. This problem is further exacerbated by the fact that permaculturists (I include myself) do not necessarily pride themselves on a tidy garden farm. Everything tends to be a "work in progress," and it shows. Such concerns notwithstanding, the color photos are particularly well done; the numbered captions are easily understood. The photos appear to have been carefully selected, and truly do add a needed dimension that bolsters the book's authoritativeness.

If they can, you can!
Finally, Bane's case studies include an up-to-the minute analysis of his own Renaissance Farm, in Bloomington, Indiana (also home to the magazine The Permaulture Activist). His year-by-year history of the progress he and partner Keith Johnson have made in turning their .7 acre into a working farm makes for genuinely interesting reading. As Bane describes the endlessly cyclical nature of what they do:
Self-reliance and food storage are both increasing. Soils are improving. The growing season is now year-round.
Would that we could all say the same.

Working examples
Other operations are described, as well: Jerome's Organics, of Basalt, Colorado; Old 99 Farm, in Dundas, Ontario; and Radical Roots Farm, of Harrisonburg, Virginia.

Jerome's is far and away the oldest of the four farms described, established in 1982. It's also different in that its primary mission is educational, both insofar as garden design is concerned, and with regard to producing successful yields. Jerome Osentowski welcomes students and visitors to his demonstration garden and educational programs year-round.

The other two garden farms were much more recently established. In the case of Old 99 Farm, operator Ian Graham sells winter vegetables, eggs, dairy and cow-shares. Radical Roots operators Dave O'Neill and wife Lee Sturgis offer annual vegetables, nursery plants, and eggs. Dave teaches permaculture design, and consults. Lee and Dave hire paid interns, affording a valuable opportunity to up-and-coming garden farmers.

I'll leave you with a parting thought of my own - this book deserves to be a part of your gardening library - and one of Peter Bane's:
The essential work of Permaculture activism is to understand and see abundance in the world around us, often before others do, and then to help others to see it also, to bring it into being.

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Review




"When Apollo 13 found itself hurtling through space on its way to the far side of the moon with a ruptured oxygen tank, a critical path was assembled that returned all souls safely back to Earth. In The Permaculture Handbook, Peter Bane has mapped the critical path to a safe landing for civilization in the 21st century. That path runs through the backyards of suburbia and across the rooftops and balconies of urban apartment houses. Like the Apollo mission, Bane has jury-rigged our carbon dioxide removal system by re-tasking other components — small scale horticulture, aquatic plants and foraged trash, for instance — to buy us breathing room. This is a must read."

— Albert Bates, author of The Post Petroleum Survival Guide and Cookbook, and The Biochar Solution.


"The Permaculture Handbook offers practical examples from the author's many years of experience, coupled with information from permaculture practitioners from around the country. This makes the guidebook particularly useful to American readers. The chapters covering the integration of multifunctional species and breeds of domestic animals and wildlife are especially note-worthy. These chapters address the sometimes under-recognized value of animal products and services in the Permaculture literature. This book is a joy to read while thinking about applications to one's own endeavors."

— Donald Bixby, DVM, Retired Executive Director of American Livestock Breeds Conservancy


"Peter Bane's characteristic generosity and mastery are on display in this long anticipated encyclopedia of permaculture knowledge and lore. The Permaculture Handbook offers a thorough treatment of the design principles and patterns that of necessity precede the positive, practical, and profitable solutions that are the hallmark of permaculture design. Bill Mollison famously taught that we can create the "Garden of Eatin' ". Peter Bane shows us how."

— Claude William Genest, Former Deputy Leader of the Green Party of Canada. Producer, Host of the Emmy nominated PBS series "Regeneration: The Art of Sustainable Living"


"As oil becomes more scarce and expensive, society must adapt by re-localizing food systems. The Permaculture Handbook offers us a set of essential conceptual and practical tools for doing this in a way that's intelligent, beautiful, and sustainable. Want to create a better world? Your backyard — and this book — are the places to start."

— Richard Heinberg, Senior Fellow, Post Carbon Institute, Author, The End of Growth


"Here is an exquisite design manual for re-inhabiting our towns and cities, transforming them into flourishing and nourishing landscapes that provide food, fiber, energy and community. As you read this book, looking out from time to time at the paved, manicured tracts we've called home, you can almost see the world around you transforming — a fruit tree here, a greenhouse there, a hill of corn, beans and squash in the corner, a photovoltaic array that charges your electric bicycle nearby. We are not in an era of despair, of coming apart. We are in an era of creativity where strong seeds grow in the very cracks in the concrete of our old ways of living. I applaud Peter for the wisdom, intelligence and hard work he has invested in his detailed, beautiful map of the land of permaculture."

— Vicki Robin, author Your Money or Your Life and Blessing the Hands that Feed Us (Viking/Penguin 2013).


"Peter Bane offers a powerful antidote to what we might call our "ephemeraculture"— the consumerist, oil-dependent, wasteful, and ruinous way of life produced by the marriage of industrialism and capitalism. In a voice at once practical and visionary, he tells how we can achieve security, practice self-reliance, and revive local economies by shifting to a regenerative form of agriculture, beginning in our own backyards. If you're hungry for hope, good food, neighborliness, conviviality, and survival skills, here is the book for you."

— Scott Russell Sanders, author of A Conservationist Manifesto.


"Morally mature cultures live well with the Earth and with each other. Peter Bane's beautifully written book lays out a path to that maturity and wisdom. Future generations will thank him — and you if you read and use the wisdom he has gathered."

— Carolyn Raffensperger, Environmental lawyer, advocate for future generations, Executive Director of the Science and Environmental Health Network


"The wealth of practical knowledge in The Permaculture Handbook is a welcome addition to North America's canon of books on permaculture design, and will serve other regions as well. Peter Bane's broad and well-tested experience in ecological living, expressed here in clear and engaging prose, will guide homeowners, gardeners, and small farmers toward designing and living in lushly productive and harmonious landscapes."

— Toby Hemenway, author of Gaia's Garden: A Guide to Home-Scale Permaculture


"A book to carry us through to Eden, this keen, comprehensive design guide with its wisdom and instruction will be indispensable to any household aiming at flourishing, soil-based self-reliance. The practice is permaculture and Peter Bane is a true master."

— Stephanie Mills, author of On Gandhi's Path and Epicurean Simplicity


"With a lifetime of Permaculture immersion under his belt, Peter Bane's contribution to domestic selfreliant security in this comprehensive handbook is nothing short of remarkable. This will empower thousands of seekers to move off the bleachers and into the game. He balances beautifully the right amount of intensive ecological information with delightful case studies and practical outworkings. A gem of a manual. Thank you, Peter."

— Joel Salatin, Author, Farmer


"There are a lot of people out there who want to know how to begin making a better world, but don't know where to begin. I can't think of a better starting point for someone who wants to restore and transform their place than Peter Bane's Permaculture Handbook. Bane has taken the single most urgent question of our times "How shall we live?" and given a real and viable answer."

— Sharon Astyk, writer, farmer, teacher and author of Making Home


"The Permaculture Handbook is worth reading and rereading not only for its depth of insight but also for its storytelling charm. Peter Bane's reflections on community-based efforts to realize permaculture's potential across entire landscapes helps us realize that this set of design principles are not vague abstractions, but something that we can smell, taste and see before our very eyes."

— Gary Paul Nabhan, ethnobotanist, writer, permaculture orchardkeeper, seed saver


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Product details

Paperback: 480 pages
Publisher: New Society Publishers; Original edition (June 26, 2012)
Language: English
ISBN-10: 0865716668
ISBN-13: 978-0865716667
Product Dimensions: 8.4 x 1 x 11 inches
Shipping Weight: 2.8 pounds (View shipping rates and policies)
Average Customer Review: 4.5 out of 5 stars 52 customer reviews
Amazon Best Sellers Rank: #103,462 in Books (See Top 100 in Books)
#86 in Books > Crafts, Hobbies & Home > Gardening & Landscape Design > Garden Design
#95 in Books > Crafts, Hobbies & Home > Gardening & Landscape Design > By Technique > Organic
#103 in Books > Science & Math > Agricultural Sciences > Sustainable Agriculture


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Iain C. Massey

4.0 out of 5 starsComprehensive, good, US-CentricDecember 22, 2012
Format: PaperbackVerified Purchase

You could do worse than treat this book as a comprehensive update of the "technique" material in Mollison's "Permaculture: A Designer's Manual". There's a lot of value, a lot of practical wisdom and a lot of updated science (soil science, agronomy, ecology, human and animal nutrition) in this big book. The comparatively recent technique of a pattern language as a further aid to design is also a welcome addition. Naturally, zones, sectors, stacking, succession and the rest of the thinking tools are still here as well. It's fascinating to see Permaculture insights elaborated and developed in a second generation literature. Helpful, too.

The reference point is the urban-fringe "garden farm", producing foods for its occupants, neighbours and local markets, rather than Mollison's upland valley-scale farmstead or hamlet. But it has always been clear that Permaculture aspirations and techniques apply at scales from apartment balconies to broad-acre farms.

I guess I can't complain about a North American perspective on climate, species, etc. Much of Mollison's work was very Australian-centric. But it would be an improvement in the Permaculture literature generally to get global. Mollison and Holmgren tended towards language like "pole-wards" instead of South for the shady side, and international climate type classifications instead of national ones. They weren't fully consistent, and sometimes the language gets awkward, but I think it's an effort worth making. This book would benefit.

Don't know what I'm talking about? Want to get an overview of what this Permaculture thing is? Don't start here. There are short, accessible books that introduce you to the body of thought and practice that this book covers in comprehensive detail.

If you've read those and want the full Monty, this is one of the very best.

Disclaimer: I'm not an accredited Permaculture designer/practitioner/teacher/whatever. The official side doesn't do much for me. Permaculture is a body of ideas, aspirations and techniques for land care/land use that I've danced with ever since I heard Mollison speak at a camp in the Australian bush in 1974.
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H.Hieronimi

5.0 out of 5 starsImportant and timely addition to my libaryJuly 15, 2012
Format: PaperbackVerified Purchase

Although allready a permacultuture pracitioner and enthusiast for more than 20 years, this one had many features new to me. Peter Bane gives us really a in-depth look of permaculture principles and practices in this great book. The Graden-Farming outlook is definietly a new feature treated in depth here, very necesary-
The only flaw (for somebody like me, who is living in mexico) is that it is 100% written for the US...but I'm so used to have to translate this kind of info to other climates and circumstances, so Im NOT taking away one star, beacuse all the rest is so great.
Timely outlook to Permaculture, practical and theorectical info, Bane is also an excelent writer, and this book is in my opinion the third book that is a must in any serious PC libary, after Mollisons Designers Manual, and Holmgrens "Principles and Pathways..."
Not to be missed, excelent for beginners and advanced...

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Matt Jones

4.0 out of 5 starsA bit heavy on the threat of impending global collapse for my tasteOctober 11, 2013
Format: PaperbackVerified Purchase

I ordered this book because I have recently been fascinated with the subject. I ordered this book as my first Permaculture book, after reading all of the positive reviews, because many of the other must-reads on the subject are out of print or prohibitively expensive.

This book has a wealth of information on Permaculture but is pretty heavy on doom and gloom worldview as well. Don't believe the cute rooster on the cover. A light, how-to on getting started with backyard Permaculture this is not. While there's a place in any book on Permaculture to lay out the many reasons why it is the best practice for our future, this book presents one predominant assumption: that a shortage of fossil fuels WILL eventually force us all to live in a much simpler manner, similar to the way our ancestors lived 100 years ago.

This assumption carries throughout the rest of the book and describes strategies for completely reinventing society to deal with the fact that we won't have transportation or be able to ship anything the way we do now. All the strategies, both for the actual agricultural aspects and the larger issues of culture in general, assume that this is very plausible and imminent. That's all well and good as a component for consideration in *a section* of a book purportedly on growing food, but when it's presented heavily throughout the remainder, it begins to look like a tinfoil hat kind of thing. A good subtitle for the book would be: "How to use Permaculture in navigating society after the fossil fuel collapse".

While I think this is absolutely a possibility, I don't think we have any idea how technology may postpone or even completely remove the threat of societal collapse due to fossil fuel dry-up. With this view, one would think that each technological advance "hurts the cause" of Permaculture because it pushes back the date of collapse a little further. But then, maybe this one potential threat to our future isn't the *only* compelling reason to put Permaculture into practice.

What if technology *does* make the fossil fuel shortage irrelevant? (The horse manure crisis of earlier centuries was averted with steam power). If the fossil fuel problem were solved with some improbable, cold-fusionish, Star Trek-style solution, we still have the problems of soil degradation, damage to the atmosphere, the relegation of farming to industry, corporate control of our food production, as well as the heavy use of chemicals and genetic engineering. Also, what about things like self-reliance, the joy of growing your own sustainable food, helping the needy, and eating more healthfully? These are all considerations that make Permaculture appealing to *me* and don't require me to jump on the apocolyptic band wagon (yet). All of these ideas are mentioned and considered in the book, but they take a major back seat to the "I Am Legend" aspect of Bane's Permaculture.

I still really enjoy the book for what it is. It has great illustrations, and there's a lot of great material on the actual growing of things and system designs. The other reviews on these aspects of the book I believe to be fair. I think this book would be much more palatable to the "idiot masses" like myself who aren't yet on board with Bane's view of our near future by including strategies for coping with collapse in a *section* of the book dedicated to that topic. Instead, topics like "redesigning your home to accommodate boarding guest workers you'll need to farm your once-suburban property after collapse" are thrown in throughout the book as if that's a very casual consideration.

I wouldn't feel comfortable sharing this book with friends who aren't already into permaculture as I feel that it would alienate them. Don't believe the happy rooster!

********************************************************************************************************************

May 2014 update: I've since acquired my own copy of Mollison's Permaculture: A Designers' Manual and am still an avid fan of permaculture. I'm currently enrolled in Geoff Lawton's online Permaculture Design Course. (I think it's absolutely worth every penny of the high cost by the way.) I say all of that just to point out that I'm not just a pedestrian reader re. permaculture who's posting a marginally negative review. Permaculture will be a major part of the rest of my life.

I still agree with what I stated in the original review. My issues with it are probably *more* pronounced having studied the subject more. You see, what really attracted me (and still does) to permaculture is how overwhelmingly *positive* it is. The world's problems are talked about everywhere, but there aren't many *solutions* offered anywhere. Permaculture is about solutions, and I don't think that any of the world's problems are addressed more fully than in the study of permaculture. The Design Manual by Mollison, itself, addresses these problems in a realistic way but is overwhelmingly positive. Also, it addresses more broadly that life is better when holistically practicing the principles of permaculture because of its benefit *now*, in addition to addressing concerns re. the future.
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M. Mindlin

4.0 out of 5 starsGreat book for the suburban permaculturistDecember 5, 2013
Format: PaperbackVerified Purchase

This is some really great work from a permaculture elder, Peter Bane. The focus is on the suburban expression of permaculture, which is probably where the majority of practitioners find themselves. However the title might lead one to think it is a more comprehensive approach, which it is not. Thus the four stars rather than five.

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larry

5.0 out of 5 starsThis is a must buy, if you are interested in Permaculture in your future.November 15, 2013
Format: PaperbackVerified Purchase

The author not only writes about this way of life but also lives it. He also tells the various stories in a clear understandable way. Plus the author has many You-tube videos to also help you see, hear and understand his message. If you have any doubt as to whether you want to purchase this book, just watch a few of his online videos. I'm sure you will have no doubts about purchasing this book. He is also a permaculture landscape architect.

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2019/01/08

Human microbiota - Wikipedia

Human microbiota - Wikipedia
Human microbiota
From Wikipedia, the free encyclopedia

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Graphic depicting the human skin microbiota, with relative prevalences of various classes of bacteria
----
The human microbiota is the aggregate of microorganisms that resides on or within any of a number of human tissues and biofluids, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary and gastrointestinal tracts. They include bacteria, archaea, fungi, protists and viruses. Though micro-animalscan also live on the human body, they are typically excluded from this definition. 
The human microbiome refers specifically to the collective genomes of resident microorganisms.[1]

Humans are colonized by many microorganisms; the traditional estimate is that the average human body is inhabited by ten times as many non-human cells as human cells, but more recent estimates have lowered that ratio to 3:1 or even to approximately the same number.[2][3][4][5] Some microorganisms that colonize humans are commensal, meaning they co-exist without harming humans; others have a mutualistic relationship with their human hosts.[1]:700[6]Conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce, like trimethylamine, which the human body converts to trimethylamine N-oxide via FMO3-mediated oxidation.[7][8] Certain microorganisms perform tasks that are known to be useful to the human host but the role of most of them is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota.[1]

The Human Microbiome Project took on the project of sequencing the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina.[1] 
It reached a milestone in 2012 when it published its initial results.[9]


Contents

1Terminology
2Relative numbers
3Study
3.1Shotgun Sequencing
3.1.1Collection of samples and DNA extraction
3.1.2Preparation of the library and sequencing
3.1.3Metagenome assembly
3.1.4Contig binning
3.1.5Analysis after the processing

3.2Marker gene analysis
3.3Phylogenetic Analysis
4Types
4.1Bacteria
4.2Archaea
4.3Fungi
4.4Viruses
5Anatomical areas
5.1Skin
5.2Conjunctiva
5.3Gut
5.4Urethra and bladder
5.5Vagina
5.6Placenta
5.7Uterus
5.8Oral cavity
5.9Lung
5.10Biliary tract
6Disease and death
6.1Cancer
6.2Inflammatory bowel disease
6.3Human immunodeficiency virus
6.4Death
7Environmental health
8Migration
9See also
10Bibliography
11References
12External links
Terminology[edit]
Life timeline
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Axis scale: million years

Also see: Human timeline and Nature timeline

Though widely known as flora ormicroflora, this is a misnomer in technical terms, since the word root flora pertains to plants, and biotarefers to the total collection of organisms in a particular ecosystem. Recently, the more appropriate term microbiota is applied, though its use has not eclipsed the entrenched use and recognition of flora with regard to bacteria and other microorganisms. Both terms are being used in different literature.[6]
Relative numbers[edit]

As of 2014, it was often reported in popular media and in the scientific literature that there are about 10 times as many microbial cells in the human body as there are human cells; this figure was based on estimates that the human microbiome includes around 100 trillion bacterial cells and that an adult human typically has around 10 trillion human cells.[2] In 2014, the American Academy of Microbiologypublished a FAQ that emphasized that the number of microbial cells and the number of human cells are both estimates, and noted that recent research had arrived at a new estimate of the number of human cells – approximately 37.2 trillion, meaning that the ratio of microbial-to-human cells, if the original estimate of 100 trillion bacterial cells is correct, is closer to 3:1.[2][3] In 2016, another group published a new estimate of the ratio being roughly 1:1 (1.3:1, with "an uncertainty of 25% and a variation of 53% over the population of standard 70-kg males").[4][5]
Study[edit]
Main article: Human Microbiome Project

Flowchart illustrating how the human microbiome is studied on the DNA level.

The problem of elucidating the human microbiome is essentially identifying the members of a microbial community which includes bacteria, eukaryotes, and viruses.[10] This is done primarily using DNA-based studies, though RNA, protein and metabolite based studies are also performed.[10][11] DNA-based microbiome studies typically can be categorized as either targeted amplicon studies or more recently shotgunmetagenomic studies. The former focuses on specific known marker genes and is primarily informative taxonomically, while the latter is an entire metagenomic approach which can also be used to study the functional potential of the community.[10] One of the challenges that is present in human microbiome studies, but not in other metagenomic studies is to avoid including the host DNA in the study.[12]

Aside from simply elucidating the composition of the human microbiome, one of the major questions involving the human microbiome is whether there is a "core", that is, whether there is a subset of the community that is shared among most humans.[13][14] If there is a core, then it would be possible to associate certain community compositions with disease states, which is one of the goals of the Human Microbiome Project. It is known that the human microbiome (such as the gut microbiota) is highly variable both within a single subject and among different individuals, a phenomenon which is also observed in mice.[6]

On 13 June 2012, a major milestone of the Human Microbiome Project (HMP) was announced by the NIH director Francis Collins.[9] The announcement was accompanied with a series of coordinated articles published in Nature[15][16] and several journals in the Public Library of Science (PLoS) on the same day. By mapping the normal microbial make-up of healthy humans using genome sequencing techniques, the researchers of the HMP have created a reference database and the boundaries of normal microbial variation in humans. From 242 healthy U.S. volunteers, more than 5,000 samples were collected from tissues from 15 (men) to 18 (women) body sites such as mouth, nose, skin, lower intestine (stool), and vagina. All the DNA, human and microbial, were analyzed with DNA sequencing machines. The microbial genome data were extracted by identifying the bacterial specific ribosomal RNA, 16S rRNA. The researchers calculated that more than 10,000 microbial species occupy the human ecosystem and they have identified 81 – 99% of the genera.
Shotgun Sequencing[edit]

It is frequently difficult to culture in laboratory communities of bacteria, archaea and viruses, therefore sequencing technologies can be exploited in metagenomics, too. Indeed, the complete knowledge of the functions and the characterization of specific microbial strains offer a great potentiality in therapeutic discovery and human health.[17]
Collection of samples and DNA extraction[edit]

The main point is to collect an amount microbial biomass that is sufficient to perform the sequencing and to minimize the sample contamination; for this reason, enrichment techniques can be used. In particular, the DNA extraction method must be good for every bacterial strain, not to have the genomes of the ones that are easy to lyse. Mechanical lysis is usually preferred rather than chemical lysis, and bead beating may result in DNAloss when preparing the library.[17]
Preparation of the library and sequencing[edit]

The most used platforms are Illumina, Ion Torrent, Oxford Nanopore MinION and Pacific Bioscience Sequel, although the Illumina platform is considered the most appealing option due to its wide availability, high output and accuracy. There are no indications regarding the correct amount of sample to use.[17]
Metagenome assembly[edit]

The de novo approach is exploited; however, it presents some difficulties to be overcome. The coverage depends on each genome abundance in its specific community; low-abundance genomes may undergo fragmentation if the sequencing depth is not sufficient enough to avoid the formation of gaps. Luckily, there are metagenome-specific assemblers to help, since, if hundreds of strains are present, the sequencing depth needs to be increased to its maximum.[17]
Contig binning[edit]

Neither from which genome every contig derives, nor the number of genomes present in the sample are known a priori; the aim of this step is to divide the contigs into species. The methods to perform such analysis can be either supervised (database with known sequences) or unsupervised (direct search for contig groups in the collected data). However, both methods require a kind of metric to define a score for the similarity between a specific contig and the group in which it must be put, and algorithms to convert the similarities into allocations in the groups.[17]
Analysis after the processing[edit]

The statistical analysis is essential to validate the obtained results (ANOVA can be used to size the differences between the groups); if it is paired with graphical tools, the outcome is easily visualized and understood.[17]

Once a metagenome is assembled, it is possible to infer the functional potential of the microbiome. The computational challenges for this type of analysis are greater than for single genomes, due the fact that usually metagenomes assemblers have poorer quality, and many recovered genes are non-complete or fragmented. After the gene identification step, the data can be used to carry out a functional annotation by means of multiple alignment of the target genes against orthologs databases.[18]
Marker gene analysis[edit]

It is a technique that exploits primers to target a specific genetic region and enables to determine the microbial phylogenies. The genetic region is characterized by a highly variable region which can confer detailed identification; it is delimited by conserved regions, which function as binding sites for primers used in PCR. The main gene used to characterize bacteria and archaea is 16S rRNA gene, while fungi identification is based on Internal Transcribed Spacer (ITS). The technique is fast and not so expensive and enables to obtain a low-resolution classification of a microbial sample; it is optimal for samples that may be contaminated by host DNA. Primer affinity varies among all DNA sequences, which may result in biases during the amplification reaction; indeed, low-abundance samples are susceptible to overamplification errors, since the other contaminating microorganisms result to be over-represented in case of increasing the PCR cycles. Therefore, the optimization of primer selection can help to decrease such errors, although it requires complete knowledge of the microorganisms present in the sample, and their relative abundances.[19]

Marker gene analysis can be influenced by the primer choice; in this kind of analysis it's desirable to use a well-validated protocol (such as the one used in the Earth Microbiome Project). The first thing to do in a marker gene amplicon analysis is to remove sequencing errors; a lot of sequencing platforms are very reliable, but most of the apparent sequence diversity is still due to errors during the sequencing process. To reduce this phenomenon a first approach is to cluster sequences into Operational taxonomic unit (OTUs): this process consolidates similar sequences (a 97% similarity threshold is usually adopted) into a single feature that can be used in further analysis steps; this method however would discard SNPs because they would get clustered into a single OTU. Another approach is Oligotyping, which includes position-specific information from 16s rRNA sequencing to detect small nucleotide variations and from discriminating between closely related distinct taxa. These methods give as an output a table of DNA sequences and counts of the different sequences per sample rather than OTU.[19]

Another important step in the analysis is to assign a taxonomic name to microbial sequences in the data. This can be done using machine learning approaches that can reach an accuracy at genus-level of about 80%. Other popular analysis packages provide support for taxonomic classification using exact matches to reference databases and should provide greater specificity, but poor sensitivity. Unclassified microorganism should be further checked for organelle sequences.[19]
Phylogenetic Analysis[edit]

Many methods that exploit phylogenetic inference use the 16SRNA gene for Archea and Bacteria and the 18SRNA gene for Eukariotes. Phylogenetic comparative methods (PCS) are based on the comparison of multiple traits among microorganisms; the principle is: the closely they are related, the higher number of traits they share. Usually PCS are coupled with phylogenetic generalized least square (PGLS) or other statistical analysis to get more significant results. Ancestral state reconstruction is used in microbiome studies to impute trait values for taxa whose traits are unknown. This is commonly performed with PICRUSt, which relies on available databases. Phylogenetic variables are chosen by researchers according to the type of study: through the selection of some variables with significant biological informations, it is possible to reduce the dimension of the data to analyse.[20]

Phylogenetic aware distance is usually performed with UniFrac or similar tools, such as Soresen's index or Rao's D, to quantify the differences between the different communities. All this methods are negatively affected by horizontal gene trasmission (HGT), since it can generate errors and lead to the correlation of distant species. There are different ways to reduce the negative impact of HGT: the use of multiple genes or computational tools to assess the probability of putative HGT events.[20]
Types[edit]
Bacteria[edit]

Populations of microbes (such as bacteria and yeasts) inhabit the skin and mucosal surfaces in various parts of the body. Their role forms part of normal, healthy human physiology, however if microbe numbers grow beyond their typical ranges (often due to a compromised immune system) or if microbes populate (such as through poor hygiene or injury) areas of the body normally not colonized or sterile (such as the blood, or the lower respiratory tract, or the abdominal cavity), disease can result (causing, respectively, bacteremia/sepsis, pneumonia, and peritonitis).[medical citation needed]

The Human Microbiome Project found that individuals host thousands of bacterial types, different body sites having their own distinctive communities. Skin and vaginal sites showed smaller diversity than the mouth and gut, these showing the greatest richness. The bacterial makeup for a given site on a body varies from person to person, not only in type, but also in abundance. Bacteria of the same species found throughout the mouth are of multiple subtypes, preferring to inhabit distinctly different locations in the mouth. Even the enterotypes in the human gut, previously thought to be well understood, are from a broad spectrum of communities with blurred taxon boundaries.[21][22]

It is estimated that 500 to 1,000 species of bacteria live in the human gut but belong to just a few phyla: Firmicutes and Bacteroidetes dominate but there are also Proteobacteria, Verrumicrobia, Actinobacteria, Fusobacteria and Cyanobacteria.[23]

A number of types of bacteria, such as Actinomyces viscosus and A. naeslundii, live in the mouth, where they are part of a sticky substance called plaque. If this is not removed by brushing, it hardens into calculus (also called tartar). The same bacteria also secrete acids that dissolve tooth enamel, causing tooth decay.

The vaginal microflora consist mostly of various lactobacillus species. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that L. iners is in fact most common, followed by L. crispatus. Other lactobacilli found in the vagina are L. jensenii, L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to infections such as bacterial vaginosis or candidiasis ("yeast infection").
Archaea[edit]

Archaea are present in the human gut, but, in contrast to the enormous variety of bacteriain this organ, the numbers of archaeal species are much more limited.[24] The dominant group are the methanogens, particularly Methanobrevibacter smithii and Methanosphaera stadtmanae.[25] However, colonization by methanogens is variable, and only about 50% of humans have easily detectable populations of these organisms.[26]

As of 2007, no clear examples of archaeal pathogens were known,[27][28] although a relationship has been proposed between the presence of some methanogens and human periodontal disease.[29]
Fungi[edit]
See also: Mycobiota (human)

Fungi, in particular yeasts, are present in the human gut.[30][31][32][33] The best-studied of these are Candida species due to their ability to become pathogenic in immunocompromised and even in healthy hosts.[31][32][33] Yeasts are also present on the skin,[30] such as Malassezia species, where they consume oils secreted from the sebaceous glands.[34][35]
Viruses[edit]
See also: Human virome

Viruses, especially bacterial viruses (bacteriophages), colonize various body sites. These colonized sites include the skin,[36] gut,[37] lungs,[38] and oral cavity.[39] Virus communities have been associated with some diseases, and do not simply reflect the bacterial communities.[40][41][42]
Anatomical areas[edit]
Main article: List of human flora
Skin[edit]
Main article: Skin flora

A study of twenty skin sites on each of ten healthy humans found 205 identified genera in nineteen bacterial phyla, with most sequences assigned to four phyla: Actinobacteria(51.8%), Firmicutes (24.4%), Proteobacteria (16.5%), and Bacteroidetes (6.3%).[43] A large number of fungal genera are present on healthy human skin, with some variability by region of the body; however, during pathological conditions, certain genera tend to dominate in the affected region.[30] For example, Malassezia is dominant in atopic dermatitis and Acremonium is dominant on dandruff-afflicted scalps.[30]

The skin acts as a barrier to deter the invasion of pathogenic microbes. The human skin contains microbes that reside either in or on the skin and can be residential or transient. Resident microorganism types vary in relation to skin type on the human body. A majority of microbes reside on superficial cells on the skin or prefer to associate with glands. These glands such as oil or sweat glands provide the microbes with water, amino acids, and fatty acids. In addition, resident bacteria that associated with oil glands are often Gram-positive and can be pathogenic.[1]
Conjunctiva[edit]

A small number of bacteria and fungi are normally present in the conjunctiva.[30][44]Classes of bacteria include Gram-positive cocci (e.g., Staphylococcus and Streptococcus) and Gram-negative rods and cocci (e.g., Haemophilus and Neisseria) are present.[44]Fungal genera include Candida, Aspergillus, and Penicillium.[30] The lachrymal glandscontinuously secrete, keeping the conjunctiva moist, while intermittent blinking lubricates the conjunctiva and washes away foreign material. Tears contain bactericides such as lysozyme, so that microorganisms have difficulty in surviving the lysozyme and settling on the epithelial surfaces.
Gut[edit]

Tryptophan metabolism by human gastrointestinal microbiota (

v
t
e)

Tryptophan
Clostridium
sporogenes

Lacto-
bacilli

Tryptophanase-
expressing
bacteria
IPA
I3A
Indole
Liver
Brain
IPA
I3A
Indole
Indoxyl
sulfate

AST-120
AhR
Intestinal
immune
cells

Intestinal
epithelium

PXR
Mucosal homeostasis:
TNF-α
Junction protein-
coding mRNAs
L cell
GLP-1
T J
Neuroprotectant:
↓Activation of glial cells and astrocytes
4-Hydroxy-2-nonenal levels
DNA damage
Antioxidant
–Inhibits β-amyloid fibril formation
Maintains mucosal reactivity:
IL-22 production
Associated with vascular disease:
Oxidative stress
Smooth muscle cellproliferation
Aortic wall thickness and calcification
Associated with chronic kidney disease:
Renal dysfunction
Uremic toxin
Kidneys
This diagram shows the biosynthesis of bioactive compounds (indole and certain other derivatives) from tryptophan by bacteria in the gut.[45] Indole is produced from tryptophan by bacteria that express tryptophanase.[45] Clostridium sporogenes metabolizes tryptophan into indole and subsequently 3-indolepropionic acid (IPA),[46] a highly potent neuroprotective antioxidant that scavenges hydroxyl radicals.[45][47][48] IPA binds to the pregnane X receptor (PXR) in intestinal cells, thereby facilitating mucosal homeostasis and barrier function.[45] Following absorption from the intestine and distribution to the brain, IPA confers a neuroprotective effect against cerebral ischemia and Alzheimer’s disease.[45]Lactobacillus species metabolize tryptophan into indole-3-aldehyde (I3A) which acts on the aryl hydrocarbon receptor (AhR) in intestinal immune cells, in turn increasing interleukin-22 (IL-22) production.[45] Indole itself triggers the secretion of glucagon-like peptide-1 (GLP-1) in intestinal L cellsand acts as a ligand for AhR.[45] Indole can also be metabolized by the liver into indoxyl sulfate, a compound that is toxic in high concentrations and associated with vascular disease and renal dysfunction.[45] AST-120 (activated charcoal), an intestinal sorbent that is taken by mouth, adsorbsindole, in turn decreasing the concentration of indoxyl sulfate in blood plasma.[45]

Main article: Gut flora
See also: Gut–brain axis

In humans the composition of gut flora is established during birth.[49] Birth by Cesarean section or vaginal delivery also influences the gut's microbial composition. Babies born through the vaginal canal have non-pathogenic, beneficial gut microbiota similar to those found in the mother.[50] However, the gut microbiota of babies delivered by C-section harbors more pathogenic bacteria such as Escherichia coli and Staphylococcus and it takes longer to develop non-pathogenic, beneficial gut microbiota.[51]

The relationship between some gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship.[1] Some human gut microorganisms benefit the host by fermentating dietary fiber into short-chain fatty acids(SCFAs), such as acetic acid and butyric acid, which are then absorbed by the host.[6][52]Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols, and xenobiotics.[1][52] The systemic importance of the SCFAs and other compounds they produce are like hormones and the gut flora itself appears to function like an endocrine organ,[52] and dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions.[6][53]

The composition of human gut flora changes over time, when the diet changes, and as overall health changes.[6][53] A systematic review of 15 human randomized controlled trialsfrom July 2016 found that certain commercially available strains of probiotic bacteria from the Bifidobacterium and Lactobacillus genera (B. longum, B. breve, B. infantis, L. helveticus, L. rhamnosus, L. plantarum, and L. casei), when taken by mouth in daily doses of 109–1010 colony forming units (CFU) for 1–2 months, possess treatment efficacy (i.e., improves behavioral outcomes) in certain central nervous system disorders – including anxiety, depression, autism spectrum disorder, and obsessive–compulsive disorder – and improves certain aspects of memory.[54] However, changes in the composition of gut microbiota has also been found to be correlated with harmful effects on health. In an article published by Musso et al., it was found that the gut microbiota of obese invidividuals had more Firmicutes and less Bacteroidetes than healthy individuals.[55] Furthermore, a study done by Gordon et al., confirmed that it was the composition of the microbiota that causes obesity rather than the other way around. This was done by transplanting the gut microbiota from diet-induced obese(DIO) mice or lean control mice into lean germ-free mice that do not have a microbiome. They found that the mice transplanted with DIO mouse gut microbiota had significantly higher total body fat than the mice transplanted with lean mouse microbiota when fed with the same diet.[56]
Urethra and bladder[edit]

The genitourinary system appears to have a microbiota,[57][58] which is an unexpected finding in light of the long-standing use of standard clinical microbiological culture methods to detect bacteria in urine when people show signs of a urinary tract infection; it is common for these tests to show no bacteria present.[59] It appears that common culture methods do not detect many kinds of bacteria and other microorganisms that are normally present.[59]As of 2017, sequencing methods were used to identify these microorganisms to determine if there are differences in microbiota between people with urinary tract problems and those who are healthy.[57][58]
Vagina[edit]
Main article: Vaginal flora
See also: List of microbiota species of the lower reproductive tract of women, List of bacterial vaginosis microbiota, and Vaginal microbiota in pregnancy

Vaginal microbiota refers to those species and genera that colonize the vagina. These organisms play an important role in protecting against infections and maintaining vaginal health.[60] The most abundant vaginal microorganisms found in premenopausal women are from the genus Lactobacillus, which suppress pathogens by producing hydrogen peroxide and lactic acid.[32][60][61] Bacterial species composition and ratios vary depending on the stage of the menstrual cycle.[62][63][needs update] Ethnicity also influences vaginal flora. The occurrence of hydrogen peroxide-producing lactobacilli is lower in African American women and vaginal pH is higher.[64] Other influential factors such as sexual intercourse and antibiotics have been linked to the loss of lactobacilli.[61] Moreover, studies have found that sexual intercourse with a condom does appear to change lactobacilli levels, and does increase the level of Escherichia coli within the vaginal flora.[61] Changes in the normal, healthy vaginal microbiota is an indication of infections, such as candidiasisor bacterial vaginosis.[61] Candida albicans inhibits the growth of Lactobacillus species, while Lactobacillus species which produce hydrogen peroxide inhibit the growth and virulence of Candida albicans in both the vagina and the gut.[30][32][33]

Fungal genera that have been detected in the vagina include Candida, Pichia, Eurotium, Alternaria, Rhodotorula, and Cladosporium, among others.[30]
Placenta[edit]
Main article: Placental microbiome

Until recently the placenta was considered to be a sterile organ but commensal, nonpathogenic bacterial species and genera have been identified that reside in the placental tissue.[65][66][67]
Uterus[edit]
Main article: Uterine microbiome

Until recently, the upper reproductive tract of women was considered to be a sterile environment. A variety of microorganisms inhabit the uterus of healthy, asymptomatic women of reproductive age. The microbiome of the uterus differs significantly from that of the vagina and gastrointestinal tract.[68]
Oral cavity[edit]
Main article: Oral microbiology

The environment present in the human mouth allows the growth of characteristic microorganisms found there. It provides a source of water and nutrients, as well as a moderate temperature.[1] Resident microbes of the mouth adhere to the teeth and gums to resist mechanical flushing from the mouth to stomach where acid-sensitive microbes are destroyed by hydrochloric acid.[1][32]

Anaerobic bacteria in the oral cavity include: Actinomyces, Arachnia, Bacteroides, Bifidobacterium, Eubacterium, Fusobacterium, Lactobacillus, Leptotrichia, Peptococcus, Peptostreptococcus, Propionibacterium, Selenomonas, Treponema, and Veillonella.[69][needs update] Genera of fungi that are frequently found in the mouth include Candida, Cladosporium, Aspergillus, Fusarium, Glomus, Alternaria, Penicillium, and Cryptococcus, among others.[30]

Bacteria accumulate on both the hard and soft oral tissues in biofilm allowing them to adhere and strive in the oral environment while protected from the environmental factors and antimicrobial agents.[70] Saliva plays a key biofilm homeostatic role allowing recolonization of bacteria for formation and controlling growth by detaching biofilm buildup.[71] It also provides a means of nutrients and temperature regulation. The location of the biofilm determines the type of exposed nutrients it receives.[72]

Oral bacteria have evolved mechanisms to sense their environment and evade or modify the host. However, a highly efficient innate host defense system constantly monitors the bacterial colonization and prevents bacterial invasion of local tissues. A dynamic equilibrium exists between dental plaque bacteria and the innate host defense system.[73]

This dynamic between host oral cavity and oral microbes plays a key role in health and disease as it provides entry into the body.[74] A healthy equilibrium presents a symbiotic relationship where oral microbes limit growth and adherence of pathogens while the host provides an environment for them to flourish.[74][70] Ecological changes such as change of immune status, shift of resident microbes and nutrient availability shift from a mutual to parasitic relationship resulting in the host being prone to oral and systemic disease.[70]Systemic diseases such as diabetes and cardiovascular diseases has been correlated to poor oral health.[74] Of particular interest is the role of oral microorganisms in the two major dental diseases: dental caries and periodontal disease.[73] Pathogen colonization at the periodontium cause an excessive immune response resulting in a periodontal pocket- a deepened space between the tooth and gingiva.[70] This acts as a protected blood-rich reservoir with nutrients for anaerobic pathogens.[70] Systemic disease at various sites of the body can result from oral microbes entering the blood bypassing periodontal pockets and oral membranes.[74]

Persistent proper oral hygiene is the primary method for preventing oral and systemic disease.[74] It reduces the density of biofilm and overgrowth of potential pathogenic bacteria resulting in disease.[72] However, proper oral hygiene may not be enough as the oral microbiome, genetics, and changes to immune response play a factor in developing chronic infections.[72] Use of antibiotics could treat already spreading infection but ineffective against bacteria within biofilms.[72]
Lung[edit]
Main article: Lung microbiome

Much like the oral cavity, the upper and lower respiratory system possess mechanical deterrents to remove microbes. Goblet cells produce mucous which traps microbes and moves them out of the respiratory system via continuously moving ciliated epithelial cells.[1] In addition, a bactericidal effect is generated by nasal mucus which contains the enzyme lysozyme.[1] The upper and lower respiratory tract appears to have its own set of microbiota.[75] Pulmonary bacterial microbiota belong to 9 major bacterial genera: Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus. Some of the bacteria considered "normal biota" in the respiratory tract can cause serious disease especially in immunocompromised individuals; these include Streptococcus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, and Staphylococcus aureus.[citation needed] Fungal genera that compose the pulmonary mycobiome include Candida, Malassezia, Neosartorya, Saccharomyces, and Aspergillus, among others.[30]

Unusual distributions of bacterial and fungal genera in the respiratory tract is observed in people with cystic fibrosis.[30][76] Their bacterial flora often contains antibiotic-resistant and slow-growing bacteria, and the frequency of these pathogens changes in relation to age.[76]
Biliary tract[edit]

Traditionally the biliary tract has been considered to be normally sterile, and the presence of microorganisms in bile is a marker of pathological process. This assumption was confirmed by failure in allocation of bacterial strains from the normal bile duct. Papers began emerging in 2013 showing that the normal biliary microbiota is a separate functional layer which protects a biliary tract from colonization by exogenous microorganisms.[77]
Disease and death[edit]

A symbiotic relationship between the gut microbiota and different bacteria may influence an individual's immune response.[78]
Cancer[edit]

Although cancer is generally a disease of host genetics and environmental factors, microorganisms are implicated in some 20% of human cancers.[79] Particularly for potential factors in colon cancer, bacterial density is one million times higher than in the small intestine, and approximately 12-fold more cancers occur in the colon compared to the small intestine, possibly establishing a pathogenic role for microbiota in colon and rectal cancers.[80] Microbial density may be used as a prognostic tool in assessment of colorectal cancers.[80]

The microbiota may affect carcinogenesis in three broad ways: (i) altering the balance of tumor cell proliferation and death, (ii) regulating immune system function, and (iii) influencing metabolism of host-produced factors, foods and pharmaceuticals.[79] Tumors arising at boundary surfaces, such as the skin, oropharynx and respiratory, digestive and urogenital tracts, harbor a microbiota. Substantial microbe presence at a tumor site does not establish association or causal links. Instead, microbes may find tumor oxygen tensionor nutrient profile supportive. Decreased populations of specific microbes or induced oxidative stress may also increase risks.[79][80] Of the around 1030 microbes on earth, ten are designated by the International Agency for Research on Cancer as human carcinogens.[79] Microbes may secrete proteins or other factors directly drive cell proliferation in the host, or may up- or down-regulate the host immune system including driving acute or chronic inflammation in ways that contribute to carcinogenesis.[79]

Concerning the relationship of immune function and development of inflammation, mucosal surface barriers are subject to environmental risks and must rapidly repair to maintain homeostasis. Compromised host or microbiota resiliency also reduce resistance to malignancy, possibly inducing inflammation and cancer. Once barriers are breached, microbes can elicit proinflammatory or immunosuppressive programs through various pathways.[79] For example, cancer-associated microbes appear to activate NF-κΒ signaling within the tumor microenviroment. Other pattern recognition receptors, such as nucleotide-binding oligomerization domain–like receptor (NLR) family members NOD-2, NLRP3, NLRP6 and NLRP12, may play a role in mediating colorectal cancer.[79] Likewise Helicobacter pylori appears to increase the risk of gastric cancer, due to its driving a chronic inflammatory response in the stomach.[79][80]
Inflammatory bowel disease[edit]

Inflammatory bowel disease consists of two different diseases: ulcerative colitis and Crohn's disease and both of these diseases present with disruptions in the gut microbiota (also known as dysbiosis). This dysbiosis presents itself in the form of decreased microbial diversity in the gut,[81][82] and is correlated to defects in host genes that changes the innate immune response in individuals.[81]
Human immunodeficiency virus[edit]

The HIV disease progression influences the composition and function of the gut microbiota, with notable differences between HIV-negative, HIV-positive, and post-ARTHIV-positive populations.[citation needed] HIV decreases the integrity of the gut epithelial barrier function by affecting tight junctions. This breakdown allows for translocation across the gut epithelium, which is thought to contribute to increases in inflammation seen in people with HIV.[83]

Vaginal microbiota plays a role in the infectivity of HIV, with an increased risk of infection and transmission when the woman has bacterial vaginosis, a condition characterized by an abnormal balance of vaginal bacteria.[84] The enhanced infectivity is seen with the increase in pro-inflammatory cytokines and CCR5 + CD4+ cells in the vagina. However, a decrease in infectivity is seen with increased levels of vaginal Lactobacillus, which promotes an anti-inflammatory condition.[83]
Death[edit]
Main article: necrobiome

With death the microbiome of the living body collapses and a different microbiome named necrobiome establishes itself. Its predictable changes over time are thought to be useful to help determine the time of death.[85][86]
Environmental health[edit]

Studies in 2009 questioned whether the decline in biota (including microfauna) as a result of human intervention might impede human health, hospital safety procedures, food product design, and treatments of disease.[87]
Migration[edit]

Preliminary research indicates that immediate changes in the microbiota may occur when a person migrates from one country to another, such as when Thai immigrants settled in the United States.[88] Losses of microbiota diversity were greater in obese individuals and children of immigrants.[88]
See also[edit]

Drug resistance
Human Microbiome Project
Human milk microbiome
Human virome
Initial acquisition of microbiota
List of bacterial vaginosis microbiota
Microbiome
Microorganism
uBiome
Microbiome Immunity Project
Carbon monoxide-releasing molecules
---------

Bibliography[edit]
Ed Yong. I Contain Multitudes: The Microbes Within Us and a Grander View of Life.368 pages, Published 9 August 2016 by Ecco, ISBN 0062368591.


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  47. Figure 1: Molecular mechanisms of action of indole and its metabolites on host physiology and disease
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  49. IPA metabolism diagram
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  51. Origin: • Endogenous • Microbial
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External links[edit]
The Secret World Inside You Exhibit 2015-2016, American Museum of Natural History
FAQ: Human Microbiome, January 2014 American Society For Microbiology

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