Understanding of the Microbiome at the Genome Level

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

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 5689

Special Issue Editors


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Guest Editor
School of Biological Sciences and Technology, Yangzhou University, Yangzhou, China
Interests: next-generation sequencing data analysis; microbiome; the interaction between the microbiome and the host and the interaction between the microbiome and specific microorganisms (such as pathogenic bacteria)
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou, China
Interests: microbiota; probiotics; mucosal immunity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A vast number of microorganisms populate host-associated environments, collectively forming microbiomes. These microbes can be broadly categorized as mutualists, pathogens, or commensals based on their interactions with the host. Mutualists play a crucial role in benefiting hosts, contributing to functions like nutrient absorption and resistance against pathogen invasion. Conversely, pathogens can induce specific diseases upon colonization. Notably, the invasion of certain pathogens can disrupt the balance of the microbiome, facilitating their infection process. Conversely, specific mutualists can mitigate and prevent pathogen invasion through direct antagonistic actions, modulation of host immune responses, and other mechanisms. A comprehensive understanding of how beneficial and pathogenic microbes interact with the host and other microorganisms is essential for developing microbiome manipulation strategies to enhance host health. As the Guest Editors of this Special Issue, we encourage the scientific community to submit contributions (original research articles, review articles, and short communications) in the following (but not exclusive) areas:

  1. Genomic research on microorganisms isolated (or recovered from metagenomic data) from the microbiomes.
  2. Genome-resolved inter-microbial interactions inside the microbiome
  3. Roles of beneficial- or pathogenicity-associated genes in the interactions of microbes with the microbiome
  4. The role of mycobiota and their interaction with bacteria
  5. The role of gut microbiota in stress (weaning stress, nutritional stress, heat stress, oxidative stress and etc.)

Prof. Dr. Yunzeng Zhang
Dr. Haoyu Liu
Guest Editors

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Keywords

  • beneficial
  • pathogenic
  • microbe
  • microbiome
  • interaction
  • genome
  • transcriptome
  • mycobiota
  • stress

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Published Papers (5 papers)

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Research

10 pages, 1009 KiB  
Article
Crown Gall Induced by a Natural Isolate of Brucella (Ochrobactrumpseudogrignonense Containing a Tumor-Inducing Plasmid
by Marjolein J. G. Hooykaas and Paul J. J. Hooykaas
Microorganisms 2025, 13(1), 102; https://doi.org/10.3390/microorganisms13010102 - 7 Jan 2025
Viewed by 552
Abstract
Crown gall disease in plants is caused by “Agrobacteria”, bacteria belonging to the Rhizobiaceae family, which carry a tumor-inducing (Ti) plasmid. Unexpectedly, we found evidence that a natural isolate from a rose crown gall, called NBC51/LBA8980, was a bacterium that did not belong [...] Read more.
Crown gall disease in plants is caused by “Agrobacteria”, bacteria belonging to the Rhizobiaceae family, which carry a tumor-inducing (Ti) plasmid. Unexpectedly, we found evidence that a natural isolate from a rose crown gall, called NBC51/LBA8980, was a bacterium that did not belong to the Rhizobiaceae family. Whole-genome sequencing revealed that this bacterium contained three large DNA circles with rRNA and tRNA genes, representing one chromosome and two chromids, respectively, and two megaplasmids, including a Ti plasmid. Average nucleotide identity (ANIb, ANIm) and genome-to-genome distance (GGDC) values above the thresholds of 96% and 70%, respectively, showed that NBC51/LBA8980 belonged to the species Brucella (Ochrobactrum) pseudogrignonense. Its Ti plasmid was almost identical to certain succinamopine Ti plasmids previously identified in Agrobacterium strains, suggesting that this Ti plasmid may have been recently acquired by NBC51/LBA8980 in the tumor environment. Full article
(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)
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25 pages, 3870 KiB  
Article
Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses
by Roland Zell, Marco Groth, Lukas Selinka and Hans-Christoph Selinka
Microorganisms 2024, 12(11), 2361; https://doi.org/10.3390/microorganisms12112361 - 19 Nov 2024
Viewed by 872
Abstract
In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete [...] Read more.
In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete and partial virus genomes up to a length of 37 kb were identified, with noda-like and reo-like viruses being most abundant, followed by bunya-like and birna-like viruses. Viruses related to the Permutotetraviridae, Nidovirales, Flaviviridae, Rhabdoviridae and Chuviridae as well as the unclassified Jῑngmén virus and Negev virus groups were also present. The results indicate a broad extent of recombinant virus genomes, supporting the concept of the modularity of eukaryotic viruses. For example, novel combinations of genes encoding replicase and structural proteins with a jellyroll fold have been observed. Less than 35 viruses could be assigned to existing virus genera. These are (i) an avian deltacoronavirus which was represented by only one short contig, albeit with 98% similarity, (ii) a seadornavirus and a rotavirus, and (iii) some 30 nodaviruses. All remaining viruses are novel and too diverse for accommodation in existing genera. Many of the virus genomes exhibit ORFans encoding hypothetical proteins of up to 2000 amino acids without conserved protein domains. Full article
(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)
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15 pages, 4532 KiB  
Article
Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis
by Linqi Wang, Qinyu Wang and Yan Zhou
Microorganisms 2024, 12(10), 2086; https://doi.org/10.3390/microorganisms12102086 - 18 Oct 2024
Viewed by 1101
Abstract
Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, [...] Read more.
Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, genetic evidence supporting this mechanism remains insufficient. In this study, we identified over 55,000 oral translocation genes (OTGs) associated with colorectal cancer (CRC) and inflammatory bowel disease (IBD). These genes are primarily involved in signal transduction and cell wall biosynthesis and show consistency in their functions between IBD and CRC. Furthermore, we found that Leclercia adecarboxylata, a newly discovered opportunistic pathogen, has a significantly high abundance in the gut microbiota of colorectal cancer patients. OTGs of this pathogen were enriched in 15 metabolic pathways, including those associated with amino acid and cofactor metabolism. These findings, for the first time, provide evidence at the genetic level of the transfer of oral pathogens to the intestine and offer new insights into the understanding of the roles of oral pathogens in the development of gastrointestinal cancers. Full article
(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)
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10 pages, 607 KiB  
Article
First Insight into the Whole Genome Sequencing Whole Variations in Mycobacterium bovis from Cattle in Morocco
by Mohammed Khoulane, Siham Fellahi, Slimane Khayi, Mohammed Bouslikhane, Hassan Lakhdissi and Jaouad Berrada
Microorganisms 2024, 12(7), 1316; https://doi.org/10.3390/microorganisms12071316 - 27 Jun 2024
Viewed by 1052
Abstract
Six cattle heads which tested positive against bovine tuberculosis (bTB) in Morocco were investigated to confirm the disease and to determine the source(s) of infection. Polymerase Chain Reaction (PCR) was directly performed on tissue samples collected from slaughtered animals. All investigated animals tested [...] Read more.
Six cattle heads which tested positive against bovine tuberculosis (bTB) in Morocco were investigated to confirm the disease and to determine the source(s) of infection. Polymerase Chain Reaction (PCR) was directly performed on tissue samples collected from slaughtered animals. All investigated animals tested positive to PCR for the Mycobacterium bovis sub-type. Bacteriological isolation was conducted according to the technique recommended by WOAH for the cultivation of the Mycobacterium tuberculosis Complex (MBTC). Whole genome sequencing (WGS) was carried out on six mycobacterial isolates and the phylogenic tree was constructed. The six Moroccan isolates fit with clades II, III, IV, V and VII and were confirmed to belong to the clonal complexes Eu2, Unknown 2 and 7 as well as to sublineages La1.7.1, La1.2 and La1.8.2. The significant Single Nucleotide Polymorphism (SNPs) ranged from 84 to 117 between the isolates and the reference M. bovis strain and from 17 to 212 between the six isolates. Considering the high resolution of WGS, these results suggests that the source of infection of the bTB could be linked to imported animals as five of the investigated reactor animals were imported a few months prior. WGS can be a useful component to the Moroccan strategy to control bTB. Full article
(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)
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16 pages, 2553 KiB  
Article
Bacillus velezensis YXDHD1-7 Prevents Early Blight Disease by Promoting Growth and Enhancing Defense Enzyme Activities in Tomato Plants
by Wangxi Li, Lili Sun, Hangtao Wu, Wenjie Gu, Yusheng Lu, Chong Liu, Jiexin Zhang, Wanling Li, Changmin Zhou, Haoyang Geng, Yaying Li, Huanlong Peng, Chaohong Shi, Dan Wang and Guixiang Peng
Microorganisms 2024, 12(5), 921; https://doi.org/10.3390/microorganisms12050921 - 30 Apr 2024
Cited by 2 | Viewed by 1492
Abstract
Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing [...] Read more.
Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing strain, Bacillus velezensis YXDHD1-7 was isolated from the tomato rhizosphere soil, which had the strongest inhibitory effect against Alternaria solani. Inoculation with bacterial suspensions of this strain promoted the growth of tomato seedlings effectively. Furthermore, inoculations at 106, 107, and 108 cfu/mL resulted in control efficacies of 100%, 83.15%, and 69.90%, respectively. Genome sequencing showed that it possesses 22 gene clusters associated with the synthesis of antimicrobial metabolites and genes that are involved in the production of IAA. Furthermore, it may be able to produce spermidine and volatile compounds that also enhance plant growth and defense responses. Our results suggest that strain YXDHD1-7 prevents early blight disease by promoting growth and enhancing the defense enzyme activities in tomato plants. This strain is a promising candidate for an excellent microbial inoculant that can be used to enhance tomato production. Full article
(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)
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