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Structure, Function and Diversity of Gut Microbes in Animals
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Structure, Function and Diversity of Gut Microbes in Animals

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 28 February 2025 | Viewed by 18838

Special Issue Editor

Dr. Priscilla Branchu

E-Mail Website
Guest Editor
IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, 31024 Toulouse, France
Interests: Enterobacteriaceae; genetic diversity; gene function; genomic evolution; host-pathogen interactions; ecological niche
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Gut microbes are a crucial part of animal health. Early in life, aerobes such as Escherichia coli colonize the gut of warm-blooded animals. This step is crucial in animal life, as early gut colonizers have been demonstrated to be involved in mechanisms such as providing an external vitamin source (e.g., E. coli providing vitamin K), but also in shaping the gut microbiota—notably by the consumption of oxygen or interactions with the host that will shape the composition and thus the main functions of the gut microbiota of animals. In adults, the imbalance of the gut microbiota community, commonly called “dysbiosis”, has been found to be involved in many diseases, such as type 2 diabetes, obesity, inflammatory bowel diseases, or even neurological diseases such as Parkinson’s or Alzheimer’s. It is noteworthy that gut microbes are not always beneficial for animals; some of them are or become pathogenic for their host under suitable conditions. This is the case, for example, of Clostridium difficile, which is carried by up to 15% of healthy adults and can be a threat for the carrier upon an antibiotic-induced dysbiosis. Interestingly, fecal transplant from healthy donors is widely used to treat C. difficile diarrhea.

We are pleased to invite you to contribute to our Special Issue, “Structure, Function and Diversity of Gut Microbes in Animals” in the Microbiology section of our journal. This Special Issue will collect manuscripts dedicated to the comprehension of the structure, function and diversity of gut microbes in animals, to reinforce the state of the art of the topic. New approaches and innovative technologies are welcome.

Dr. Priscilla Branchu
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. Biology 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

  • microbes
  • gut
  • function
  • structure
  • diversity
  • benefit
  • pathogenesis
  • dysbiosis

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Published Papers (7 papers)

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Research

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23 pages, 4764 KiB  
Article
Sex-Induced Changes in Microbial Eukaryotes and Prokaryotes in Gastrointestinal Tract of Simmental Cattle
by Diórman Rojas, Richard Estrada, Yolanda Romero, Deyanira Figueroa, Carlos Quilcate, Jorge J. Ganoza-Roncal, Jorge L. Maicelo, Pedro Coila, Wigoberto Alvarado and Ilse S. Cayo-Colca
Biology 2024, 13(11), 932; https://doi.org/10.3390/biology13110932 - 15 Nov 2024
Viewed by 354
Abstract
This study investigates gender-based differences in the gut microbiota of Simmental cattle, focusing on bacterial, archaeal, and fungal communities. Fecal samples were collected and analyzed using high-throughput sequencing, with taxonomic classification performed through the SILVA and UNITE databases. Alpha and beta diversity metrics [...] Read more.
This study investigates gender-based differences in the gut microbiota of Simmental cattle, focusing on bacterial, archaeal, and fungal communities. Fecal samples were collected and analyzed using high-throughput sequencing, with taxonomic classification performed through the SILVA and UNITE databases. Alpha and beta diversity metrics were assessed, revealing significant differences in the diversity and composition of archaeal communities between males and females. Notably, females exhibited higher alpha diversity in archaea, while beta diversity analyses indicated distinct clustering of bacterial and archaeal communities by gender. The study also identified correlations between specific microbial taxa and hematological parameters, with Treponema and Methanosphaera showing gender-specific associations that may influence cattle health and productivity. These findings highlight the importance of considering gender in microbiota-related research and suggest that gender-specific management strategies could optimize livestock performance. Future research should explore the role of sex hormones in shaping these microbial differences. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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18 pages, 3870 KiB  
Article
Dynamic Analysis of Stool Microbiota of Simmental Calves and Effects of Diarrhea on Their Gut Microbiota
by Qianxun Wang, Mula Na, Shiyu Jia, Miao Sun, Song Gao, Shiwei Pan, Wu Dong, Yang Song and Jingfeng Yang
Biology 2024, 13(7), 520; https://doi.org/10.3390/biology13070520 - 13 Jul 2024
Viewed by 969
Abstract
The objective of this study was to explore the dynamic changes in the gut microbiota of Simmental calves before weaning and to compare the microbial composition and functionality between healthy calves and those with diarrhea. Fourteen neonatal Simmental calves were divided into a [...] Read more.
The objective of this study was to explore the dynamic changes in the gut microbiota of Simmental calves before weaning and to compare the microbial composition and functionality between healthy calves and those with diarrhea. Fourteen neonatal Simmental calves were divided into a healthy group (n = 8) and a diarrhea group (n = 6). Rectal stool samples were collected from each calf on days 1, 3, 5, 7, 9, 12, 15, 18, 22, 26, 30, 35, and 40. High-throughput sequencing of the 16S rRNA gene V1–V9 region was conducted to examine changes in the gut microbiota over time in both groups and to assess the influence of diarrhea on microbiota structure and function. Escherichia coli, Bacteroides fragilis, and B. vulgatus were the top three bacterial species in preweaning Simmental calves. Meanwhile, the major functions of the fecal microbiota included “metabolic pathways”, “biosynthesis of secondary metabolites”, “biosynthesis of antibiotics”, “microbial metabolism in diverse environments”, and “biosynthesis of amino acids”. For calves in the healthy group, PCoA revealed that the bacterial profiles on days 1, 3, 5, 7, and 9 differed from those on days 15, 18, 22, 26, 30, 35, and 40. The profiles on day 12 clustered with both groups, indicating that microbial structure changes increased with age. When comparing the relative abundance of bacteria between healthy and diarrheic calves, the beneficial Lactobacillus johnsonii, Faecalibacterium prausnitzii, and Limosilactobacillus were significantly more abundant in the healthy group than those in the diarrhea group (p < 0.05). This study provides fundamental insights into the gut microbiota composition of Simmental calves before weaning, potentially facilitating early interventions for calf diarrhea and probiotic development. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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17 pages, 2473 KiB  
Article
A Long-Chain Dextran Produced by Weissella cibaria Boosts the Diversity of Health-Related Gut Microbes Ex Vivo
by Maria Tintoré, Jordi Cuñé, Lam Dai Vu, Jonas Poppe, Pieter Van den Abbeele, Aurélien Baudot and Carlos de Lecea
Biology 2024, 13(1), 51; https://doi.org/10.3390/biology13010051 - 18 Jan 2024
Cited by 4 | Viewed by 2439
Abstract
Long-chain dextrans are α-glucans that can be produced by lactic acid bacteria. NextDextTM, a specific long-chain dextran with a high degree of polymerisation, produced using Weissella cibaria, was recently shown to exert prebiotic potential in vitro. In this study, the [...] Read more.
Long-chain dextrans are α-glucans that can be produced by lactic acid bacteria. NextDextTM, a specific long-chain dextran with a high degree of polymerisation, produced using Weissella cibaria, was recently shown to exert prebiotic potential in vitro. In this study, the ex vivo SIFR® technology, recently validated to provide predictive insights into gut microbiome modulation down to the species level, was used to investigate the effects of this long-chain dextran on the gut microbiota of six human adults that altogether covered different enterotypes. A novel community modulation score (CMS) was introduced based on the strength of quantitative 16S rRNA gene sequencing and the highly controlled ex vivo conditions. This CMS overcomes the limitations of traditional α-diversity indices and its application in the current study revealed that dextran is a potent booster of microbial diversity compared to the reference prebiotic inulin (IN). Long-chain dextran not only exerted bifidogenic effects but also consistently promoted Bacteroides spp., Parabacteroides distasonis and butyrate-producing species like Faecalibacterium prausnitzii and Anaerobutyricum hallii. Further, long-chain dextran treatment resulted in lower gas production compared to IN, suggesting that long-chain dextran could be better tolerated. The additional increase in Bacteroides for dextran compared to IN is likely related to the higher propionate:acetate ratio, attributing potential to long-chain dextran for improving metabolic health and weight management. Moreover, the stimulation of butyrate by dextran suggests its potential for improving gut barrier function and inflammation. Overall, this study provides a novel tool for assessing gut microbial diversity ex vivo and positions long-chain dextran as a substrate that has unique microbial diversity enhancing properties. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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13 pages, 674 KiB  
Article
Effects of Fumarate and Nitroglycerin on In Vitro Rumen Fermentation, Methane and Hydrogen Production, and on Microbiota
by Jichao Li, Shengwei Zhao, Zhenxiang Meng, Yunlong Gao, Jing Miao, Shengyong Mao and Wei Jin
Biology 2023, 12(7), 1011; https://doi.org/10.3390/biology12071011 - 15 Jul 2023
Cited by 2 | Viewed by 1898
Abstract
This study aimed to investigate the effects of fumarate and nitroglycerin on rumen fermentation, methane and hydrogen production, and microbiota. In vitro rumen fermentation was used in this study with four treatment groups: control (CON), fumarate (FA), nitroglycerin (NG) and fumarate plus nitroglycerin [...] Read more.
This study aimed to investigate the effects of fumarate and nitroglycerin on rumen fermentation, methane and hydrogen production, and microbiota. In vitro rumen fermentation was used in this study with four treatment groups: control (CON), fumarate (FA), nitroglycerin (NG) and fumarate plus nitroglycerin (FN). Real-time PCR and 16S rRNA gene sequencing were used to analyze microbiota. The results showed that nitroglycerin completely inhibited methane production and that this resulted in hydrogen accumulation. Fumarate decreased the hydrogen accumulation and improved the rumen fermentation parameters. Fumarate increased the concentration of propionate and microbial crude protein, and decreased the ratio of acetate to propionate in FN. Fumarate, nitroglycerin and their combination did not affect the abundance of bacteria, protozoa and anaerobic fungi, but altered archaea. The PCoA showed that the bacterial (Anosim, R = 0.747, p = 0.001) and archaeal communities (Anosim, R = 0.410, p = 0.005) were different among the four treatments. Compared with CON, fumarate restored Bacteroidetes, Firmicutes, Spirochaetae, Actinobacteria, Unclassified Ruminococcaceae, Streptococcus, Treponema and Bifidobacterium in relative abundance in FN, but did not affect Succinivibrio, Ruminobacter and archaeal taxa. The results indicated that fumarate alleviated the depressed rumen fermentation caused by the inhibition of methanogenesis by nitroglycerin. This may potentially provide an alternative way to use these chemicals to mitigate methane emission in ruminants. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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16 pages, 5959 KiB  
Article
Short-Term Alternate Feeding between Terrestrially Sourced Oil- and Fish Oil-Based Diets Modulates the Intestinal Microecology of Juvenile Turbot
by Xiuhua Ma, Yaoyao Kong, Houguo Xu, Qingzhu Bi, Mengqing Liang, Kangsen Mai and Yanjiao Zhang
Biology 2023, 12(5), 650; https://doi.org/10.3390/biology12050650 - 26 Apr 2023
Cited by 1 | Viewed by 1778
Abstract
A nine-week feeding trial was conducted to investigate changes in the intestinal microbiota of turbot in response to alternate feeding between terrestrially sourced oil (TSO)- and fish oil (FO)-based diets. The following three feeding strategies were designed: (1) continuous feeding with the FO-based [...] Read more.
A nine-week feeding trial was conducted to investigate changes in the intestinal microbiota of turbot in response to alternate feeding between terrestrially sourced oil (TSO)- and fish oil (FO)-based diets. The following three feeding strategies were designed: (1) continuous feeding with the FO-based diet (FO group); (2) weekly alternate feeding between soybean oil (SO)- and FO-based diets (SO/FO group); and (3) weekly alternate feeding between beef tallow (BT)- and FO-based diets (BT/FO group). An intestinal bacterial community analysis showed that alternate feeding reshaped the intestinal microbial composition. Higher species richness and diversity of the intestinal microbiota were observed in the alternate-feeding groups. A PCoA analysis showed that the samples clustered separately according to the feeding strategy, and among the three groups, the SO/FO group clustered relatively closer to the BT/FO group. The alternate feeding significantly decreased the abundance of Mycoplasma and selectively enriched specific microorganisms, including short-chain fatty acid (SCFA)-producing bacteria, digestive bacteria (Corynebacterium and Sphingomonas), and several potential pathogens (Desulfovibrio and Mycobacterium). Alternate feeding may maintain the intestinal microbiota balance by improving the connectivity of the ecological network and increasing the competitive interactions within the ecological network. The alternate feeding significantly upregulated the KEGG pathways of fatty acid and lipid metabolism, glycan biosynthesis, and amino acid metabolism in the intestinal microbiota. Meanwhile, the upregulation of the KEGG pathway of lipopolysaccharide biosynthesis indicates a potential risk for intestinal health. In conclusion, short-term alternate feeding between dietary lipid sources reshapes the intestinal microecology of the juvenile turbot, possibly resulting in both positive and negative effects. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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Review

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14 pages, 1432 KiB  
Review
Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease
by Maria Ines Moreira de Gouveia, Annick Bernalier-Donadille and Gregory Jubelin
Biology 2024, 13(3), 142; https://doi.org/10.3390/biology13030142 - 23 Feb 2024
Cited by 11 | Viewed by 6765
Abstract
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in [...] Read more.
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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30 pages, 2685 KiB  
Review
Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production
by Harpreet Kaur, Gurjeet Kaur, Taruna Gupta, Deepti Mittal and Syed Azmal Ali
Biology 2023, 12(9), 1200; https://doi.org/10.3390/biology12091200 - 1 Sep 2023
Cited by 12 | Viewed by 3661
Abstract
Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the [...] Read more.
Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact. Full article
(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)
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