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Microorganisms
Special Issues
Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition
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Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 1016

Special Issue Editor

Dr. Lifeng Zhu

E-Mail Website
Guest Editor
College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
Interests: gut microbiome metagenome; microbial ecology; phylogeography; population genetic structure; landscape genetics; adaptive; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, "Gut Microbiota: Metagenomics to Study Ecology".

Microorganisms is pleased to solicit manuscripts for a Special Issue on “Gut Microbiota: Metagenomics to Study Ecology”, with Guest Editors Lifeng Zhu. This Special Issue is targeted towards metagenomic (including multi-omics) research of the gut microbiome, involved in all aspects of ecology. The gut microbiome plays a vital role in host nutrition intake, the immune system, and health. Metagenomics has greatly advanced our understanding of gut microbial composition (metagenomic assembled genomes) and function (community genomics and microbiomics), which has helped to reveal the ecological interaction between the gut microbiome and host. Further, metagenomics could shed light on the host local adaptation (e.g., diet and harsh environment). We will consider original scientific research articles, comprehensive reviews, comments, commentaries, and perspectives for publication. Topics of interest include gut microbial ecology, multi-omics studies, microbial genomics, host–microbe interactions, host local adaptation, and biodiversity conservation, all in relation to gut metagenomics. All manuscripts will be peer reviewed.

Dr. Lifeng Zhu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metagenomics
  • ecology
  • multi-omics
  • metagenomic assembled genomes
  • function
  • host–microbe interactions
  • behavior
  • local adaptation
  • biodiversity conservation

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Related Special Issue

Published Papers (2 papers)

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Research

20 pages, 1434 KiB  
Article
Gut Microbiome Development in Rock Pigeons: Effects of Food Restriction Early in Life
by Maurine W. Dietz, Bin-Yan Hsu, Marco van der Velde and B. Irene Tieleman
Microorganisms 2025, 13(6), 1191; https://doi.org/10.3390/microorganisms13061191 - 23 May 2025
Abstract
The developmental period is a critical phase in birds, influencing even lifetime reproductive success. The gut microbiome (GM) is important herein, affecting digestive capacity and immune function. Diet impacts the GM, but wild nestlings may experience resource limitations, which may also affect the [...] Read more.
The developmental period is a critical phase in birds, influencing even lifetime reproductive success. The gut microbiome (GM) is important herein, affecting digestive capacity and immune function. Diet impacts the GM, but wild nestlings may experience resource limitations, which may also affect the GM. We investigated the effects of a week of food restriction early in life on the GM in captive rock pigeon nestlings (Columba livia). We sampled the GM at 0, 2, 4, 7, 8, 12, 20, 27, and 38 days and in foster parents. Alpha diversity varied only with age. However, differences in alpha diversity between nestlings and adults were larger during food restriction. Beta diversity varied with age, food treatment, and their interaction term. Four of the eleven major genera varied with age, while four others did not vary with age or food treatment. Major genera that contained potential pathogens (Escherichia-Shigella and Clostridium sensu stricto 1) were more abundant under food restriction. Food restriction thus affected GM development. The increase in alpha diversity and potential pathogens suggest that suppressed immune function may mediate the impact of food restriction on the GM. The effect diminished when food restriction was ended, suggesting that in wild nestlings, the impact of food restriction on the GM may be short-term. Full article
(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition)
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11 pages, 1090 KiB  
Communication
Causal Association Between the Mucosal and Luminal Microbiotas from the Gastrointestinal Tract of Weaned Piglets Using Bayesian Network
by Shu Yoshimura, Takamitsu Tsukahara, Toru Takahashi, Hiroto Miura, So Morishima, Masaaki Kise, Jiye Shin, Yoshihiro Yahara and Ryo Inoue
Microorganisms 2025, 13(2), 256; https://doi.org/10.3390/microorganisms13020256 - 24 Jan 2025
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Abstract
The aim of this study was to investigate the microbiota composition and its potential interactions across seven gut locations (stomachs, jejuna, ilea, ceca, proximal colons, distal colons, and recta) in weaned pigs to identify key influencing microbiotas. To compare between microbiota compositions, 16S [...] Read more.
The aim of this study was to investigate the microbiota composition and its potential interactions across seven gut locations (stomachs, jejuna, ilea, ceca, proximal colons, distal colons, and recta) in weaned pigs to identify key influencing microbiotas. To compare between microbiota compositions, 16S rRNA gene amplicon sequencing was performed. Six 70-day-old healthy crossbred (Duroc × Large White × Landrace) piglets were introduced as donors. A Bayesian network (BN) was used to examine the directional interactions among the microbiotas evaluated (seven mucosal and seven digesta microbiotas). Based on edge connectivity frequency, the microbiota in jejunal mucosa was the central hub node, influencing other microbiotas, especially the mucosal microbiotas of the ileum, cecum, distal colon, and rectum. The jejunal mucosa was dominated by Prevotella and lactobacilli, both recognized for their contributions to pig health. Among Prevotella, Prevotella copri and Prevotella sp. were predominant in jejunal mucosa (4.6% and 2.9%, respectively). Lactobacilli, including eight distinct species, were distributed throughout the gastrointestinal tract. Notably, Ligilactobacillus salivarius and Lactobacillus amylovorus, known as immune-enhancing bacteria, were abundant in jejunal mucosa (1.0% and 0.8%) and digestas (0.9% and 19.2%), respectively. The BN identified rectal mucosa and digestas as two terminal nodes, influenced by upstream microbiotas in the gastrointestinal tract. This finding supports the link between fecal microbiota and pig productivity, as the fecal microbiota, closely resembling the rectal microbiota, reflects the conditions of the microbiota throughout the gastrointestinal tract. Full article
(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition)
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