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Microorganisms
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Microbiome Research for Animal, Plant and Environmental Health
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Microbiome Research for Animal, Plant and Environmental Health

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

Deadline for manuscript submissions: 15 July 2024 | Viewed by 4177

Special Issue Editors

Dr. Alex Galanis

E-Mail Website
Guest Editor
Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: probiotics; microbiota; microbiome; beneficial microbes; multi-omics; lactic acid bacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Aglaia Pappa

E-Mail Website
Guest Editor
Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: natural products; probiotics; microbiome; rhizobiome; cellular stress responses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial communities play an integral role in the homeostasis and physiology of macro- and micro-ecosystems. Accumulating evidence demonstrates the critical impact of human microbiota on health and disease. In this context, it is recognized that the host microbiota contributes to crucial processes, such as nutrient synthesis and digestion, immunomodulation, intestinal barrier integrity, and protection against pathogenic insults, while exerting extraintestinal, systemic effects. By extension, microbiota research is of great interest because of its potential applications in the field of agriculture and animal husbandry. Indeed, the soil microbiome, as well as the plant microbiome and the rhizosphere microbiome (rhizobiome) can influence plant health, nutritional value, and the ability of plants to adapt to and withstand extreme environmental conditions, thus having major ecological and economic implications. In addition, the correlation between microbiota composition and the spread of pathogens to animals and the food chain is gaining increasing attention, in the context of the “One Health” approach. Manipulating the composition of microbiota in these ecosystems can have a significant impact on human and animal health, while contributing to sustainable agriculture.

As Guest Editors of this Special Issue, we would like to invite you to submit original research articles, review articles and short communications on various aspects of animal, plant, environmental or soil microbiome research, new mechanistic insights into host–microbe interactions, methods of microbiome manipulation, and innovative technologies for sustainable livestock and agri-food production.

Dr. Alex Galanis
Dr. Aglaia Pappa
Guest Editors

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

  • environmental microbiome
  • soil microbiome
  • rhizobiome
  • host–microbe interactions
  • microbiome manipulation
  • sustainable agriculture
  • One Health

Published Papers (5 papers)

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Research

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14 pages, 1468 KiB  
Article
Unveiling a Listeria monocytogenes Outbreak in a Rabbit Farm: Clinical Manifestation, Antimicrobial Resistance, Genomic Insights and Environmental Investigation
by Inês C. Rodrigues, Marisa Ribeiro-Almeida, Leonor Silveira, Joana C. Prata, André Pinto de Carvalho, Carla Roque, João Paulo Gomes, Vítor Borges, Ângela Pista and Paulo Martins da Costa
Microorganisms 2024, 12(4), 785; https://doi.org/10.3390/microorganisms12040785 - 12 Apr 2024
Viewed by 659
Abstract
Listeria monocytogenes poses a threat to both human and animal health. This work describes an L. monocytogenes outbreak in a Portuguese rabbit farm, detailing the isolates’ clinical manifestations, necropsy findings, and phenotypic and genomic profiles. Clinical signs, exclusively observed in does, included lethargy [...] Read more.
Listeria monocytogenes poses a threat to both human and animal health. This work describes an L. monocytogenes outbreak in a Portuguese rabbit farm, detailing the isolates’ clinical manifestations, necropsy findings, and phenotypic and genomic profiles. Clinical signs, exclusively observed in does, included lethargy and reproductive signs. Post-mortem examination of does revealed splenomegaly, hepatomegaly with a reticular pattern, pulmonary congestion, and haemorrhagic lesions in the uterus, with thickening of the uterine wall and purulent greyish exudates. Positive L. monocytogenes samples were identified in fattening and maternity units across different samples, encompassing does and environmental samples. Core-genome Multi Locus Sequence Typing (cgMLST) analysis confirmed the outbreak, with the 16 sequenced isolates (lineage II, CC31, and ST325) clustering within a ≤2 allelic difference (AD) threshold. Antimicrobial susceptibility testing for five antibiotics revealed that 15 out of 19 outbreak isolates were resistant to sulfamethoxazole-trimethoprim (SXT). Concordantly, all SXT-resistant sequenced isolates were found to exclusively harbour a plasmid containing a trimethoprim-resistance gene (dfrD), along with loci linked to resistance to lincosamides (lnuG), macrolides (mphB), and polyether ionophores (NarAB operon). All sequenced outbreak isolates carried the antibiotic resistance-related genes tetM, fosX, lin, norB, lmrB, sul, and mprF. The outbreak cluster comprises isolates from does and the environment, which underscores the ubiquitous presence of L. monocytogenes and emphasizes the importance of biosecurity measures. Despite limited data on listeriosis in rabbit farming, this outbreak reveals its significant impact on animal welfare and production. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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15 pages, 2648 KiB  
Article
Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis
by Dmitry Deryabin, Christina Lazebnik, Ludmila Vlasenko, Ilshat Karimov, Dianna Kosyan, Alexander Zatevalov and Galimzhan Duskaev
Microorganisms 2024, 12(4), 747; https://doi.org/10.3390/microorganisms12040747 - 7 Apr 2024
Viewed by 838
Abstract
The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community’s variants in chickens’ ceca and to explore the most significant association [...] Read more.
The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community’s variants in chickens’ ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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11 pages, 2718 KiB  
Article
One Step Forwards in Knowledge of Blossom Blight Brown Rot Disease: Monilinia spp. SSR Marker Database
by Raminta Antanynienė, Vidmantas Stanys and Birutė Frercks
Microorganisms 2024, 12(3), 605; https://doi.org/10.3390/microorganisms12030605 - 18 Mar 2024
Viewed by 732
Abstract
A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the [...] Read more.
A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the bioinformatics tool Genome-wide Microsatellite Analyzing Toward Application (GMATA). The database provides information about SSR markers: forward and reverse sequences of the primers, fragment sizes, SSR motifs (and repeats), and the exact locations with the coordinates in the reference genome. This database currently contains information about 39,216 SSR motifs and 26,366 markers. In total, eight primers generated in silico were validated experimentally and they are marked in the database. All scientists can join this collaboration by adding their experimental data. This database is the initial start of organizing Monilinia spp. molecular data worldwide and, in the future, it could be extended by adding more molecular and genomic information. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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16 pages, 3116 KiB  
Article
Spatiotemporal Dynamics of Assyrtiko Grape Microbiota
by Konstantinos Tegopoulos, Theodora Tsirka, Christos Stekas, Eleni Gerasimidi, George Skavdis, Petros Kolovos and Maria E. Grigoriou
Microorganisms 2024, 12(3), 577; https://doi.org/10.3390/microorganisms12030577 - 14 Mar 2024
Viewed by 807
Abstract
Vitis vinifera, an economically significant grapevine species, is known for wine, juice, and table grape production. The berries of wine grapes host a diverse range of microorganisms influencing both grapevine health and the winemaking process. Indigenous to Greece, the emblematic variety Assyrtiko, [...] Read more.
Vitis vinifera, an economically significant grapevine species, is known for wine, juice, and table grape production. The berries of wine grapes host a diverse range of microorganisms influencing both grapevine health and the winemaking process. Indigenous to Greece, the emblematic variety Assyrtiko, renowned for high-quality white wines, originated from Santorini and spread to various Greek regions. Despite existing studies on the microbiota of several varieties, the carposphere microbiota of Assyrtiko grapes remains unexplored. Thus, we conducted a spatiotemporal metagenomic study to identify the epiphytic microbial community composition of Assyrtiko grapes. The study was conducted in two consecutive vintage years (2019 and 2020) across three different and distinct viticulture regions in Greece (Attica, Thessaloniki, Evros). We performed amplicon sequencing, targeting the 16S rRNA gene for bacteria and the ITS region for fungi, with subsequent comprehensive bioinformatic analysis. Our data indicate that the distribution and relative abundance of the epiphytic carposphere microbial communities of the Assyrtiko variety are shaped both by vintage and biogeography. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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Review

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11 pages, 951 KiB  
Review
Progress in Research on the Gut Microflora of the Red Panda (Ailurus fulgens)
by Xing Zhao, Zejun Zhang, Le Wang, Qian Zhang, Liwen Kang, Jia Wang, Juejie Long and Mingsheng Hong
Microorganisms 2024, 12(3), 478; https://doi.org/10.3390/microorganisms12030478 - 27 Feb 2024
Viewed by 763
Abstract
Animals can adapt to unique feeding habits through changes in the structure and function of the gut microflora. However, the gut microflora is strongly influenced by the evolutionary relationships between the host, nutritional intake, intake of microorganisms, etc. The red panda (Ailurus [...] Read more.
Animals can adapt to unique feeding habits through changes in the structure and function of the gut microflora. However, the gut microflora is strongly influenced by the evolutionary relationships between the host, nutritional intake, intake of microorganisms, etc. The red panda (Ailurus fulgens), an herbivorous carnivore, has adapted to consuming bamboo through seasonal foraging strategies and optimization of the composition and function of its gut microflora during long-term evolution. However, to date, studies of the gut bacteria of the red panda have mainly focused on the composition, diversity and function of the gut microflora of captive individuals. There are a lack of studies on how the wild red panda adapts to the consumption of bamboo, which is high in fibre and low in nutrients, through the gut microflora. This paper reviews the technology and methods used in published studies investigating the gut microflora of the red panda, as well as the composition, diversity and function of the identified microbes and the influencing factors. Furthermore, this paper suggests future research directions regarding the methodology employed in analyzing the red panda gut microflora, the interplay between gut microflora and the health of the red panda, the red panda’s adaptation to its gut microflora, and the implications of these studies for the management and conservation of wild red pandas. The goal of this review is to provide a reference for the protection of wild red pandas from the perspective of the gut microflora. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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