Amazing stuff! What little we still know about the gastrointestinal tract! Note that this is not a poop study!
The article also goes on to discuss the GI tract of ants and mice.
Poor animals again:
"Dissecting wombats’ intestines isn’t the easiest way to get an idea about what’s happening with their gut microbiomes ... for a recent study. Collecting poop would have been easier—particularly for endangered species like wombats ..."
"... characterized the microbial biogeography, or the spatial information about what microbes are present where, of the gastrointestinal (GI) tracts of one bare-nosed wombat (Vombatus ursinus) and one southern hairy-nosed wombat (Lasiorhinus latifrons) ...
For instance, in both animals, the distal end of the colon near the anus shared less than 20 percent of the microbial species of the proximal end near the small intestine. ... And the communities found in each of the animals’ proximal colons were more similar to each other than they were to the communities in the distal colon of the same animal. ...
The differences identified so far in microbial communities across the gut indicate that microbial biogeography may have functional consequences ...
The main challenge is that it’s hard to look inside a place as well protected as the gut, she explains. Euthanizing animal models is usually necessary, while for humans, biopsies of different spots in the GI tract are needed to examine those tissues and their associated microbes. But preparing for biopsies usually includes a laxative regimen that clears out the GI tract and is likely to bias the results. ...
using microfluidics to simulate the environment of the gut and capture the real time dynamics of its biogeography. These so-called “gut-on-a-chip” devices allow researchers to seed human or mouse epithelial cells onto a transparent chip, where they produce mucus, and then introduce bacteria to watch how the microbes interact with the gut cells. ..."
For instance, in both animals, the distal end of the colon near the anus shared less than 20 percent of the microbial species of the proximal end near the small intestine. ... And the communities found in each of the animals’ proximal colons were more similar to each other than they were to the communities in the distal colon of the same animal. ...
The differences identified so far in microbial communities across the gut indicate that microbial biogeography may have functional consequences ...
The main challenge is that it’s hard to look inside a place as well protected as the gut, she explains. Euthanizing animal models is usually necessary, while for humans, biopsies of different spots in the GI tract are needed to examine those tissues and their associated microbes. But preparing for biopsies usually includes a laxative regimen that clears out the GI tract and is likely to bias the results. ...
using microfluidics to simulate the environment of the gut and capture the real time dynamics of its biogeography. These so-called “gut-on-a-chip” devices allow researchers to seed human or mouse epithelial cells onto a transparent chip, where they produce mucus, and then introduce bacteria to watch how the microbes interact with the gut cells. ..."
From the abstract:
"Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account."
Figure 5: Heat map of the microbial genera that were found to be differentially abundant between proximal and distal colon sites.
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