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Research article
Seungkoo Lee
Kangwon National University School of Medicine
Corresponding Author
ORCiD: https://orcid.org/0000-0003-1317-4133
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location specific manner.
Results: We first investigated the environmental conditions at 6 different locations along the along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different location of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific location and feces, we thoroughly analyzed the composition of microbiome of the GI contents and feces. Metagenome sequencing on the GI contents and feces showed presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE richness, Shannon diversity and Fisher’s alpha all indicated that the diversities of gut microbiota at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ilium while highest in cecum and colon. Interestingly, the diversities of fecal microbiome were lower than those of cecum and colon. Beta diversity analyses by NMDS plots, PCA, and un-supervised hierarchical clustering all showed that the microbiome compositions were very diverse in location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that fecal microbiome did not represent the microbiome of the whole GI tract
Conclusion: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to the baseline assumption in the large majority of contemporary microbiome research work.
Keywords
gut microbiome, α- diversity, β-diversity
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CURRENT STATUS: Published
View the published article at BMC Microbiology.
No community comments so far
Review #1 received
Received 17 Dec, 2020
Reviewer #1 agreed
On 28 Nov, 2020
Reviewers invited
Invitations sent on 26 Nov, 2020
Editor assigned
On 04 Nov, 2020
Submission checks complete
On 04 Nov, 2020
Editor invited
On 04 Nov, 2020
Version 1
Posted 18 Aug, 2020
No comments provided
Review #2 received
Received 20 Oct, 2020
Editorial decision: Major revision
On 20 Oct, 2020
Reviewer #2 agreed
On 02 Oct, 2020
Review #1 received
Received 29 Sep, 2020
Reviewers invited
Invitations sent on 10 Sep, 2020
Reviewer #1 agreed
On 10 Sep, 2020
Editor assigned
On 13 Aug, 2020
Submission checks complete
On 12 Aug, 2020
Editor invited
On 12 Aug, 2020
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
See the published version of this preprint at BMC Microbiology.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Seungkoo Lee
Kangwon National University School of Medicine
Corresponding Author
ORCiD: https://orcid.org/0000-0003-1317-4133
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Microbiology.
No community comments so far
Review #1 received
Received 17 Dec, 2020
Reviewer #1 agreed
On 28 Nov, 2020
Reviewers invited
Invitations sent on 26 Nov, 2020
Editor assigned
On 04 Nov, 2020
Submission checks complete
On 04 Nov, 2020
Editor invited
On 04 Nov, 2020
Version 1
Posted 18 Aug, 2020
No comments provided
Review #2 received
Received 20 Oct, 2020
Editorial decision: Major revision
On 20 Oct, 2020
Reviewer #2 agreed
On 02 Oct, 2020
Review #1 received
Received 29 Sep, 2020
Reviewers invited
Invitations sent on 10 Sep, 2020
Reviewer #1 agreed
On 10 Sep, 2020
Editor assigned
On 13 Aug, 2020
Submission checks complete
On 12 Aug, 2020
Editor invited
On 12 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Microbiology.
Background: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location specific manner.
Results: We first investigated the environmental conditions at 6 different locations along the along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different location of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific location and feces, we thoroughly analyzed the composition of microbiome of the GI contents and feces. Metagenome sequencing on the GI contents and feces showed presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE richness, Shannon diversity and Fisher’s alpha all indicated that the diversities of gut microbiota at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ilium while highest in cecum and colon. Interestingly, the diversities of fecal microbiome were lower than those of cecum and colon. Beta diversity analyses by NMDS plots, PCA, and un-supervised hierarchical clustering all showed that the microbiome compositions were very diverse in location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that fecal microbiome did not represent the microbiome of the whole GI tract
Conclusion: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to the baseline assumption in the large majority of contemporary microbiome research work.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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