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The initiation of gut flora come from maternal cervical and vaginal flora (Bezirtzoglou, 1997)1. These predominantly include facultative anaerobes (e.g., Staphylococcus, Enterobacteriaceae and Streptococcus). Birth by caesarean section can cause problems because these bacteria are not passed on in the usual manner. Vael et al. (2011)2 found an association ...


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The gastrointestinal tract of a normal fetus is sterile. During birth and rapidly thereafter, bacteria from the mother and the surrounding environment colonize the infant's gut. Immediately after vaginal delivery, babies may have bacterial strains derived from the mothers' feces in the upper gastrointestinal tract.[15] Infants born by caesarean section may ...


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Edit: Matters Arising In this Nature News article, Scientists bust myth that our bodies have more bacteria than human cells, and in the bioRxiv pre-print article, Revised estimates for the number of human and bacteria cells in the body, a new estimate of the ratio of microbial cells on the human body to human cells that make up the body has been revised ...


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Heated Honey and HMF In this paper, Studies on the physicochemical characteristics of heated honey, honey mixed with ghee and their food consumption pattern by rats, by Annapoorani, et.al.;International Quarterly Journal of Research in Ayurveda, 2010 Apr-Jun; 31(2): 141–146.doi: 10.4103/0974-8520.72363, the report finds a statistically significant increase ...


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I am not sure what you read as you have not supplied any references, but humans are not 90% bacterial cells. (OP subsequently provided; see Edit 2) Humans are 100% human cells, however for every one human cell, approximately 10 single celled organisms (Bacteria or Fungi) live in (colloquially) or on the human body. This is referred to as the microbiome. You ...


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Most of the initial colonisation is said to be coincidental ('happenstance' as the textbook puts it!) exposure. It's then fairly predictable depending on: type of delivery (as Larry commented); feeding; and receipt of antibiotics. In terms of feeding, there are differences in flora between babies fed human milk and those that are given cow's milk. ...


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does the microbiome affect food metabolism? Most definitely (and not surprisingly). The Arumugam paper [1] notes that The drivers of [enterotype 1] seem to derive energy primarily from carbohydrates and proteins through fermentation, … because genes encoding enzymes involved in the degradation of these substrates (galactosidases, hexosaminidases, ...


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Yes, the microbiome affects food metabolism and the diet affects the composition of the microbiome. +1 to Konrad for his response. This is an area of research in which I and colleagues are engaged. Frankly, it is easier to assess the changes to the microbiome based on diet rather than looking at the fecal material to determine (unused) metabolic energy or ...


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Could you suggest a good source for beginners. - Louis Somers The interactions between the human body and its microbiome are quite complex. I am going to provide you with an answer that will be based on your comment that you would like an answer from a beginners perspective. For simplicity sake I will keep the answer to humans as the host organism, though ...


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Nonpathogenic E.coli are a component of the gut microbiome of humans and many other organisms. They are commensals, meaning that when they remain in the areas they have evolved to live in, and when they do not acquire virulence factors, they are benign. They live in our digestive tract and basically do nothing to harm us. In fact, commensal microorganisms ...


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From studies, lactic acid bacteria were found to be more resistant to GP (garlic powder) compared to the clostridial members of the gut microbiota. While for most bacteria the antimicrobial effect was transient, the lactobacilli showed a degree of resistance to garlic, indicating that its consumption may favour the growth of these beneficial ...


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First, you present as fact that antibiotics therapy (say AT) does not reduce weight. To show this fact, a study must weigh persons before AT and after. Confounders to this measurement are 1. weight differences because of bladder content (up to around 1 liter urine = 1kg), 2. weight differences because of bowel content (100g-200g), 3. Food weight (up to 2kg ...


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It's not like a strain of E. coli that may cause disease in immunosuppressed individuals yet is a part of normal microbiota for other people. Well, actually, it is kind of like that. The answer is complicated, but can be boiled down to, virulent serotypes of Neisseria meningitidis infect susceptible populations. For the short answer, just read between the ...


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I am going to try answer it. Bacteria in general has different survival tactics. In general for bacteria the best way how to surviva is as much copies as it cans. So imagine situation, when bacteria is surround with others bacteria. Then the race will bega. All bacteria wants to survive with same tactic as i mentioned. Thats mean the best way how to archived ...


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E. coli do not serve a human function but live inside our digestive system because our bodies can't prevent bacteria like them from living there. They live there because they can prosper and reproduce there. Most strains of E. coli do not cause problems for us, and by being part of the normal bacterial population in our gut they out-compete other, ...


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If your question is, indeed, I'm asking about the nature of sponges, and if it's a good idea to use them to wash dishes and I'd like to stay focused on that. I can answer that. I like the sponge+mesh scrubber for washing dishes (not countertops or other) because the sponge conforms to the shape of things and reaches into crevices (with dishsoap and ...


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There is some interesting information here from the Human Microbiome Project, but no details regarding the source of vaginal microflora. I would say that the sources would be gut and skin. Ethical issues of manipulating a baby's microbiome are brought to light here.


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I think the definition in Wikipedia is simply bad because it depends on another debatable definition. I prefer something which follows from an observation made by Ricard Dawkins in The Extended Phenotype (the following is my definition, but I think Dawkins had something similar in mind): An organism is any system of components which depend on each other ...


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This .csv files (comma-separated value) can be imported into Galaxy (usegalaxy.org) I recommend that you take a look at that web app, it has many build in applications for analysis. Also this site has a lot of quick video tutorials.


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The data that you are pointing to are files in .csv (comma-separated value) format. They can be opened, after downloading, by any standard spreadsheet programme, including Excel, as well as programmatically (e.g. in Python using the csv module) Apologies if you understood this and were asking for something more.


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The gut microbiome is extremely complicated, and almost anything related to it is only partially known, therefore prone to oversimplification. Trying to explain the phenomenon of gut fermentation syndrome in such a limited fashion (age, gender, ethnicity, quantity of one particular yeast, etc.) will not help us understand it. Common yeasts (C. albicans, C....


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I actually work in the same group as Chris (QIIME author), so I hope this helps: An explanation he gave to us a while back about the basis of rarefaction curves is just to give an indication of whether your sampling is reaching saturated diversity, when comparing 2 unequal samples. If you compare 2 samples, where sample x has less information (reads/...


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In general, you extract DNA, then PCR out the 16rRNA coding regions and finally sequence them. Here some links http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068739 https://support.illumina.com/content/dam/illumina-marketing/documents/products/other/16s-metagenomics-...


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Antibiotics can cause weight loss, though, especially as they are used in the clinically, they are more likely to cause weight gain than weight loss. This Lancet Infectious Diseases review is not a very good review in general, but it does catalogue many of the weight related changes in response to antibiotic therapy. You could use the references as a good ...


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The QIIME 2 tutorials are the place to get started - see here.


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If your body was filled with highly specialized bacteria living in nutrient-rich conditions, what you suggest could happen*. But in practice, you're not filled with such bacteria, and most of the bacteria in your body are living in rather harsh conditions for rapid metabolism. That said, gut bacteria do produce a range of other useful nutrients. Look for ...


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There are multiple parts to an answer for this. 1) There is not only a microbiome in the gut. So microbiomes in general are very diverse. A fish microbiome on the scales will of course be very different to the one on a human skin. 2) Gut microbiomes are also quite different both in taxonomic and functional content, as they are in different ecological ...


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I think this will vary greatly depending on the source environment. Your example (marine viruses) is probably due to the large diversity of ocean viruses of which most have no reference genome. Referencing the Human Microbiome Project: A total of 57.6% of the high-quality microbial reads could be associated with a known genome (ranging from 33–77% for ...


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I just wanted to tackle the interesting numbers here. So there are roughly 10^13 human cells in our body, and 10^14 bacterial. That is where your 90% bacteria number comes from. But remember that bacterial cells are much, much smaller than human cells. E. coli ranges from 0.5um to 2um. Human cells are ~100X larger at 0.1mm or 100um. That translates to:...


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It is an open question and an active area of research. You will not be able to get a definitive answer to your question of number, as each new discovery will add to the total. As for repopulating, we have not even determined all of the strains of microbes that populate us, many are very difficult to culture in vitro, and we do not know of all the functions ...


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