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Microorganisms
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The Genetic and Biochemical Diversity of Gut Microbiota
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The Genetic and Biochemical Diversity of Gut Microbiota

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 10823

Special Issue Editor

Dr. Dmitry G. Alexeev

E-Mail Website
Guest Editor
Department of Information Technologies, ITMO University, 197101 St. Petersburg, Russia
Interests: microbiome; inflammation; polysaccharides; fermentation; mucin restoration; probiotics

Special Issue Information

Dear Colleagues,

Research in the gut microbiome is moving from data accumulation to integration, and more and more comprehensive models are created to encompass diversity of interactions between nutrition, gut microbiome, and the host. NGS data provide insights into the tremendous diversity of metabolic potential in microbial community; biochemical profiling of nutrition and drug components, microbial media, and human samples help toward the discovery of novel active compounds, compounds created through interactions of human and microbial enzymes acting on complex substrates; and finally, the resulting compounds are able to participate in novel metabolic circles as well as start cascades of immune, endocrine, neurotrophic, and stress-response reactions.

The objective of this Special Issue is to provoke discussion aimed at knowledge integration and to represent the diversity of pathways entangled in the holobiont. We invite microbiome researchers to elaborate on existing issues of food and fiber digestion, drug metabolism, polyphenol bioconversion, neuroendocrine metabolites, and human–microbial gene interaction in health and disease, with a focus on describing the pathways interactions in more detail, presenting current unsolved issues, and stating unmet needs in holobiont research.

Bioinformatic approaches to complex system analysis and biochemical research papers are both welcome to demonstrate the interdisciplinary nature of the field and state-of-the-art in the gut microbiome field.

Dr. Dmitry G. Alexeev
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

  • bioconversion
  • host–microbiome interactions
  • microbiome diversity
  • microbial enzymes
  • microbiota-accessible carbohydrates

Published Papers (4 papers)

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Research

25 pages, 5981 KiB  
Article
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome
by German A. Ashniev, Sergey N. Petrov, Stanislav N. Iablokov and Dmitry A. Rodionov
Microorganisms 2022, 10(4), 740; https://doi.org/10.3390/microorganisms10040740 - 30 Mar 2022
Cited by 13 | Viewed by 2971
Abstract
The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some [...] Read more.
The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some amino acids (auxotrophs), while other members possess complete biosynthetic pathways for these nutrients (prototrophs). Metabolite exchange between auxotrophs and prototrophs affects microbial community structure. Previous studies of amino acid biosynthetic phenotypes were limited to model species or narrow taxonomic groups of bacteria. We analyzed over 2800 genomes representing 823 cultured HGM species with the aim to reconstruct biosynthetic pathways for proteinogenic amino acids. The genome context analysis of incomplete pathway variants allowed us to identify new potential enzyme variants in amino acid biosynthetic pathways. We further classified the studied organisms with respect to their pathway variants and inferred their prototrophic vs. auxotrophic phenotypes. A cross-species comparison was applied to assess the extent of conservation of the assigned phenotypes at distinct taxonomic levels. The obtained reference collection of binary metabolic phenotypes was used for predictive metabolic profiling of HGM samples from several large metagenomic datasets. The established approach for metabolic phenotype profiling will be useful for prediction of overall metabolic properties, interactions, and responses of HGM microbiomes as a function of dietary variations, dysbiosis and other perturbations. Full article
(This article belongs to the Special Issue The Genetic and Biochemical Diversity of Gut Microbiota)
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8 pages, 954 KiB  
Communication
Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests
by Sylvie Buffet-Bataillon, Guillaume Rizk, Vincent Cattoir, Mohamed Sassi, Vincent Thibault, Jennifer Del Giudice and Jean-Pierre Gangneux
Microorganisms 2022, 10(4), 711; https://doi.org/10.3390/microorganisms10040711 - 25 Mar 2022
Cited by 7 | Viewed by 2682
Abstract
Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies [...] Read more.
Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies with an innovative and significant approach consisting of processing steps and quality assessment for interpreting metagenomics data used for diagnosis. Here, we propose a methodology for taxon identification and abundance assessment of shotgun sequencing data of microbes that are well fitted for clinical setup. Processing steps of quality controls have been developed in order (i) to avoid low-quality reads and sequences, (ii) to optimize abundance thresholds and profiles, (iii) to combine classifiers and reference databases for best classification of species and abundance profiles for both prokaryotic and eukaryotic sequences, and (iv) to introduce external positive control. We find that the best strategy is to use a pipeline composed of a combination of different but complementary classifiers such as Kraken2/Bracken and Kaiju. Such improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies. Full article
(This article belongs to the Special Issue The Genetic and Biochemical Diversity of Gut Microbiota)
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13 pages, 1830 KiB  
Article
The Abundance of Human Milk Oligosaccharide (HMO)-Metabolizing Genes in Fecal Samples from Six-Month-Old Human Infants
by Lynn E. Ferro, Kameron Y. Sugino, Vanja Klepac-Ceraj and Sarah S. Comstock
Microorganisms 2021, 9(7), 1352; https://doi.org/10.3390/microorganisms9071352 - 22 Jun 2021
Cited by 1 | Viewed by 2054
Abstract
Herein, we report the abundance and prevalence of HMO-metabolizing genes, specifically those of Bifidobacterium infantis, in fecal samples from human infants. Forty dyads were enrolled, and each mother collected a fecal sample from her infant at six months of age. Genomic DNA [...] Read more.
Herein, we report the abundance and prevalence of HMO-metabolizing genes, specifically those of Bifidobacterium infantis, in fecal samples from human infants. Forty dyads were enrolled, and each mother collected a fecal sample from her infant at six months of age. Genomic DNA was extracted, and quantitative real-time PCR was used to determine gene abundance. The mode of delivery was not associated with gene abundance. Several gene regions, Sia (a sialidase), B. inf (16S), and GH750 (a glycoside hydrolase), were more abundant in the feces of human milk-fed infants (p < 0.05). Others, Sia and HC bin (16S), tended to be less abundant when a larger percentage of an infant’s diet consisted of solids (p < 0.10). When accounting for solid food intake, human milk exposure was positively associated with Sia and B. inf (p < 0.05) and tended to be related to the abundance of the GH750 and HC bin (p < 0.10) gene regions. With further development and validation in additional populations of infants, these assays could be used to group samples by dietary exposure even where no record of dietary intake exists. Thus, these assays would provide a method by which infant human milk intake can be assessed quickly in any well-equipped molecular biology laboratory. Full article
(This article belongs to the Special Issue The Genetic and Biochemical Diversity of Gut Microbiota)
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15 pages, 1601 KiB  
Article
Physiological and Genomic Analysis of Bacillus pumilus UAMX Isolated from the Gastrointestinal Tract of Overweight Individuals
by José Luis Reyes-Cortes, Alejandro Azaola-Espinosa, Luis Lozano-Aguirre and Edith Ponce-Alquicira
Microorganisms 2021, 9(5), 1076; https://doi.org/10.3390/microorganisms9051076 - 17 May 2021
Cited by 2 | Viewed by 2200
Abstract
The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of Bacillus pumilus UAMX (BP-UAMX) isolated from overweight individuals using genomic tools. Specifically, we assessed its ability to metabolize various carbon sources, its resistance to low pH exposure, and [...] Read more.
The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of Bacillus pumilus UAMX (BP-UAMX) isolated from overweight individuals using genomic tools. Specifically, we assessed its ability to metabolize various carbon sources, its resistance to low pH exposure, and its growth in the presence of bile salts. The genomic and bioinformatic analyses included the prediction of gene and protein metabolic functions, a pan-genome and phylogenomic analysis. BP-UAMX survived at pH 3, while bile salts (0.2–0.3% w/v) increased its growth rate. Moreover, it showed the ability to metabolize simple and complex carbon sources (glucose, starch, carboxymethyl-cellulose, inulin, and tributyrin), showing a differentiated electrophoretic profile. Genome was assembled into a single contig, with a high percentage of genes and proteins associated with the metabolism of amino acids, carbohydrates, and lipids. Antibiotic resistance genes were detected, but only one beta-Lactam resistance protein related to the inhibition of peptidoglycan biosynthesis was identified. The pan-genome of BP-UAMX is still open with phylogenetic similarities with other Bacillus of human origin. Therefore, BP-UAMX seems to be adapted to the intestinal environment, with physiological and genomic analyses demonstrating the ability to metabolize complex carbon sources, the strain has an open pan-genome with continuous evolution and adaptation. Full article
(This article belongs to the Special Issue The Genetic and Biochemical Diversity of Gut Microbiota)
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