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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: 31 January 2025 | Viewed by 15398

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

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Published Papers (12 papers)

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Research

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21 pages, 301 KiB  
Article
Deciphering Hyperammonia-Producing Bacteria (HAB) in the Rumen of Water Buffaloes (Bubalus bubalis) and Their Inhibition through Plant Extracts and Essential Oils
by Yendrembam Mery Chanu, Shyam Sundar Paul, Avijit Dey and Jerome Andonissamy
Microorganisms 2024, 12(10), 2040; https://doi.org/10.3390/microorganisms12102040 - 9 Oct 2024
Viewed by 810
Abstract
Hyperammonia-producing bacteria (HAB) are a class of microbes present in the stomach of ruminants, responsible for the rapid rate of ammonia production from protein degradation beyond the capacity of these animals for their utilization. Thus, ruminant nutritionists are interested in decreasing ruminal protein [...] Read more.
Hyperammonia-producing bacteria (HAB) are a class of microbes present in the stomach of ruminants, responsible for the rapid rate of ammonia production from protein degradation beyond the capacity of these animals for their utilization. Thus, ruminant nutritionists are interested in decreasing ruminal protein degradation and ammonia genesis by focusing on controlling the activity of HAB. The investigations of the present study were carried out to determine predominant hyperammonia-producing bacteria in the rumen of buffaloes, their isolation and characterization, as well as the inhibition of these isolates with various sources of plant secondary compounds (tannins, saponins, and essential oils). Studies employing high-throughput sequencing of amplicons of the 16S rRNA gene from genomic DNA recovered from enrichment culture of HAB of buffalo rumina indicated that, at the phylum level, Proteobacteria (61.1 to 68.2%) was the most predominant HAB. Acidaminococcus was most predominant among the identified genera. In vitro experiments were conducted with enrichment culture of buffalo rumen contents incubated with different types of feed additives such as essential oils (eucalyptus oil, lemon grass oil, and clove oil) and extracts of plants (Sapindus mukorossi fruits and Ficus bengalensis leaves), each at graded dose levels. The reduction in ammonia production by clove and lemon grass oils was evident due to the presence of major bioactive compounds, especially eugenol and limonene, which have strong antimicrobial activity. However, clove oil and Indian soapberry/reetha (Sapindus mukorossi) fruit were found to be promising and effective in reducing the growth, protease production, and ammonia production of HAB culture. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
21 pages, 11997 KiB  
Article
The Catalog of Microbial Genes and Metagenome-Assembled Genomes from the Gut Microbiomes of Five Typical Crow Species on the Qinghai–Tibetan Plateau
by Boyu Tang, You Wang, Yonggang Dong, Quanchao Cui, Zhanhao Zeng, Shunfu He, Wenxin Zhao, Zhuoma Lancuo, Shaobin Li and Wen Wang
Microorganisms 2024, 12(10), 2033; https://doi.org/10.3390/microorganisms12102033 - 8 Oct 2024
Viewed by 700
Abstract
While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the [...] Read more.
While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai–Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows’ digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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19 pages, 3614 KiB  
Article
Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba
by Manon Denux, Maickel Armenteros, Laura Weber, Carolyn A. Miller, Kinga Sántha and Amy Apprill
Microorganisms 2024, 12(9), 1822; https://doi.org/10.3390/microorganisms12091822 - 3 Sep 2024
Viewed by 788
Abstract
Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the [...] Read more.
Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean’s ‘Crown Jewel’ reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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21 pages, 6732 KiB  
Article
Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics
by Sarah Daakour, David R. Nelson, Weiqi Fu, Ashish Jaiswal, Bushra Dohai, Amnah Salem Alzahmi, Joseph Koussa, Xiaoluo Huang, Yue Shen, Jean-Claude Twizere and Kourosh Salehi-Ashtiani
Microorganisms 2024, 12(8), 1720; https://doi.org/10.3390/microorganisms12081720 - 20 Aug 2024
Viewed by 1313
Abstract
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 [...] Read more.
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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16 pages, 1686 KiB  
Article
Impact of Biotic and Abiotic Factors on Listeria monocytogenes, Salmonella enterica, and Enterohemorrhagic Escherichia coli in Agricultural Soil Extracts
by Dimple Sharma, Autumn L. Kraft, Joshua O. Owade, Mateja Milicevic, Jiyoon Yi and Teresa M. Bergholz
Microorganisms 2024, 12(7), 1498; https://doi.org/10.3390/microorganisms12071498 - 22 Jul 2024
Viewed by 1091
Abstract
Outbreaks of Enterohemorrhagic Escherichia coli (EHEC), Salmonella enterica, and Listeria monocytogenes linked to fresh produce consumption pose significant food safety concerns. These pathogens can contaminate pre-harvest produce through various routes, including contaminated water. Soil physicochemical properties and flooding can influence pathogen survival [...] Read more.
Outbreaks of Enterohemorrhagic Escherichia coli (EHEC), Salmonella enterica, and Listeria monocytogenes linked to fresh produce consumption pose significant food safety concerns. These pathogens can contaminate pre-harvest produce through various routes, including contaminated water. Soil physicochemical properties and flooding can influence pathogen survival in soils. We investigated survival of EHEC, S. enterica, and L. monocytogenes in soil extracts designed to represent soils with stagnant water. We hypothesized pathogen survival would be influenced by soil extract nutrient levels and the presence of native microbes. A chemical analysis revealed higher levels of total nitrogen, phosphorus, and carbon in high-nutrient soil extracts compared to low-nutrient extracts. Pathogen survival was enhanced in high-nutrient, sterile soil extracts, while the presence of native microbes reduced pathogen numbers. A microbiome analysis showed greater diversity in low-nutrient soil extracts, with distinct microbial compositions between extract types. Our findings highlight the importance of soil nutrient composition and microbial dynamics in influencing pathogen behavior. Given key soil parameters, a long short-term memory model (LSTM) effectively predicted pathogen survival. Integrating these factors can aid in developing predictive models for pathogen persistence in agricultural systems. Overall, our study contributes to understanding the complex interplay in agricultural ecosystems, facilitating informed decision-making for crop production and food safety enhancement. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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13 pages, 2064 KiB  
Article
Insights into the Gut Microbiome of the South American Leaf-Toed Gecko (Phylodactylus gerropygus) Inhabiting the Core of the Atacama Desert
by Daniela S. Rivera, Valentina Beltrán, Ignacio Gutiérrez-Cortés, Constanza Vargas and Fernando D. Alfaro
Microorganisms 2024, 12(6), 1194; https://doi.org/10.3390/microorganisms12061194 - 13 Jun 2024
Viewed by 1018
Abstract
Living in arid environments presents unique challenges to organisms, including limited food and water, extreme temperatures, and UV exposure. Reptiles, such as the South American leaf-toed gecko (Phyllodactylus gerrhopygus), have evolved remarkable adaptations to thrive in such harsh conditions. The gut [...] Read more.
Living in arid environments presents unique challenges to organisms, including limited food and water, extreme temperatures, and UV exposure. Reptiles, such as the South American leaf-toed gecko (Phyllodactylus gerrhopygus), have evolved remarkable adaptations to thrive in such harsh conditions. The gut microbiome plays a critical role in host adaptation and health, yet its composition remains poorly characterized in desert reptiles. This study aimed to characterize the composition and abundance of the gut microbiome in P. gerrhopygus inhabiting the hyperarid Atacama Desert, taking into account potential sex differences. Fecal samples from adult female and male geckos were analyzed by 16S rRNA gene amplicon sequencing. No significant differences in bacterial alpha diversity were observed between the sexes. However, the phylum Bacteroidota was more abundant in females, while males had a higher Firmicutes/Bacteroidota ratio. The core microbiome was dominated by the phyla Bacteroidota, Firmicutes, and Proteobacteria in both sexes. Analysis of bacterial composition revealed 481 amplicon sequence variants (ASVs) shared by female and male geckos. In addition, 108 unique ASVs were exclusive to females, while 244 ASVs were unique to males. Although the overall bacterial composition did not differ significantly between the sexes, certain taxa exhibited higher relative abundances in each sex group. This study provides insight into the taxonomic structure of the gut microbiome in a desert-adapted reptile and highlights potential sex-specific differences. Understanding these microbial communities is critical for elucidating the mechanisms underlying host resilience in Earth’s most arid environments, and for informing conservation efforts in the face of ongoing climate change. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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14 pages, 5178 KiB  
Article
The Impact of Environmental Gaseous Pollutants on the Cultivable Bacterial and Fungal Communities of the Aerobiome
by Madelaine Mejías, Romina Madrid, Karina Díaz, Ignacio Gutiérrez-Cortés, Rodrigo Pulgar and Dinka Mandakovic
Microorganisms 2024, 12(6), 1103; https://doi.org/10.3390/microorganisms12061103 - 29 May 2024
Viewed by 956
Abstract
Understanding air microbial content, especially in highly polluted urban areas, is crucial for assessing its effect on human health and ecosystems. In this context, the impact of gaseous pollutants on the aerobiome remains inconclusive due to a lack of studies separating this factor [...] Read more.
Understanding air microbial content, especially in highly polluted urban areas, is crucial for assessing its effect on human health and ecosystems. In this context, the impact of gaseous pollutants on the aerobiome remains inconclusive due to a lack of studies separating this factor from other contaminants or environmental factors. In this study, we aimed to experimentally assess the influence of contrasting concentrations of atmospheric gaseous pollutants as isolated variables on the composition of the aerobiome. Our study sites were contrasting Air Quality Index (AQI) sites of the Metropolitan Region of Chile, where nitric oxide (NO) was significantly lower at the low-AQI site than at the high-AQI site, while ozone (O3) was significantly higher. Cultivable aerobiome communities from the low-AQI site were exposed to their own pollutants or those from the high-AQI site and characterized using high-throughput sequencing (HTS), which allowed comparisons between the entire cultivable communities. The results showed increased alpha diversity in bacterial and fungal communities exposed to the high-AQI site compared to the low-AQI site. Beta diversity and compositional hierarchical clustering analyses revealed a clear separation based on NO and O3 concentrations. At the phylum level, four bacterial and three fungal phyla were identified, revealing an over-representation of Actinobacteriota and Basidiomycota in the samples transferred to the high-AQI site, while Proteobacteria were more abundant in the community maintained at the low-AQI site. At the functional level, bacterial imputed functions were over-represented only in samples maintained at the low-AQI site, while fungal functions were affected in both conditions. Overall, our results highlight the impact of NO and/or O3 on both taxonomic and functional compositions of the cultivable aerobiome. This study provides, for the first time, insights into the influence of contrasting pollutant gases on entire bacterial and fungal cultivable communities through a controlled environmental intervention. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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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 1462
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
Cited by 3 | Viewed by 2095
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 1260
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
Cited by 1 | Viewed by 1440
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
Cited by 2 | Viewed by 1631
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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