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When Genes Meet Microbial Ecology and Evolution

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (10 February 2023) | Viewed by 32481

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Special Issue Editor

Dr. Renmao Tian

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Guest Editor

Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60501, USA
Interests: microbial genomics; environmental microbiology; microbial ecology; bioinformatics; machine learning
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

When genes meet microbial ecology and evolution, there are so many stories happening.

Microbial communities, being the largest part of the Earth’s biodiversity, play an important role in the biogeochemical cycles of the planet and support for life. The discipline microbial ecology studies the diversity, structure, and distribution of microbial communities, as well as their interaction with each other and with environmental factors. Microbial evolution explores the adaptation of microorganisms to the environment via genetic change under selective pressure.

Different from the traditional ecology of macro-organisms, the microbial species cannot be quantified through counting due to the small size of cells. To overcome this barrier, gene-based technologies have been used to quantify the relative abundances of species in a community in a highly efficient way. For example, 16S rRNA gene amplicon sequencing has been applied in studies of community composition and can quantify thousands of species in multiple samples with a single round of sequencing. With the technologies of genes, many theories and hypotheses of the traditional ecology and evolution will be tested for the microbial world.

This Special Issue, entitled ‘When Genes Meet Microbial Ecology and Evolution’, tells stories of microbial ecology and evolution using gene-based technologies (marker gene amplicon, genome, transcriptome, etc.). It will cover topics of but not be limited to microbial genomics, environmental microbiology, microbial diversity, host–microbe interaction, medical microbiology, and any other fields in the scope of microbial ecology and evolution. As a kind reminder, you are encouraged to apply or expand theories (or hypothesis) of ecology and evolution in your studies to improve readability.

Dr. Renmao Tian
Guest Editor

Manuscript Submission Information

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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. Genes 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 2600 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

microbial genomics
environmental microbiology
microbial diversity
host–microbe interaction
medical microbiology

Published Papers (12 papers)

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Research

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24 pages, 4079 KiB

Open AccessArticle

From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors

by Karine Villeneuve, Michel Violette and Cassandre Sara Lazar

Genes 2023, 14(1), 1; https://doi.org/10.3390/genes14010001 - 20 Dec 2022

Cited by 3 | Viewed by 1506

Abstract

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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13 pages, 2625 KiB

Open AccessArticle

Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria

by Xiangyang Li, Zilin Yang, Guohui Zhang, Shengli Si, Xianzhi Wu and Lin Cai

Genes 2022, 13(11), 2149; https://doi.org/10.3390/genes13112149 - 18 Nov 2022

Cited by 3 | Viewed by 1430

Abstract

Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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17 pages, 2911 KiB

Open AccessArticle

Integrated Analysis of the Fecal Metagenome and Metabolome in Bladder Cancer in a Chinese Population

by Chuan Qin, Zhenghao Chen, Rui Cao, Mingjun Shi and Ye Tian

Genes 2022, 13(11), 1967; https://doi.org/10.3390/genes13111967 - 28 Oct 2022

Cited by 4 | Viewed by 1835

Abstract

Bladder cancer (BLCA) is a common malignancy of the urinary system. The gut microbiome produces various metabolites that play functional roles in tumorigenesis and tumor progression. However, the integrative analysis of the gut microbiome and metabolome in BLCA has still been lacking. Thus, the aim of this study was to identify microbial and functional characteristics and metabolites in BLCA in a Chinese population. Metagenomics, targeted metabolomics, bioinformatics, and integrative analysis were used in fecal samples of BLCA patients and healthy individuals. We found gut microbiomes were significantly dysregulated in BLCA patients, including Bifidobacterium, Lactobacillus, Streptococcus, Blautia, and Eubacterium. We also found 11Z-eicosenoic acid, 3-methoxytyrosine, abrine, aniline-2-sulfonate, arachidic acid, conjugated linoleic acids, elaidic acid, glycylleucine, glycylproline, leucyl-glycine, linoelaidic acid, linoleic acid, nicotinamide hypoxanthine dinucleotide, oleic acid, petroselinic acid, and ricinoleic acid to be significantly decreased, while cholesterol sulfate was significantly increased in BLCA patients. Integration of metagenomics and metabolomics revealed interactions between gut microbiota and metabolites and the host. We identified the alterations of gut microbiomes and metabolites in BLCA in a Chinese population. Moreover, we preliminarily revealed the associations between specific gut microbiomes and metabolites. These findings determined potential causative links among gut dysbiosis, dysregulated metabolites, and BLCA. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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13 pages, 2141 KiB

Open AccessArticle

The Light Chain Domain and Especially the C-Terminus of Receptor-Binding Domain of the Botulinum Neurotoxin (BoNT) Are the Hotspots for Amino Acid Variability and Toxin Type Diversity

by Renmao Tian, Melissa Widel and Behzad Imanian

Genes 2022, 13(10), 1915; https://doi.org/10.3390/genes13101915 - 21 Oct 2022

Cited by 1 | Viewed by 1835

Abstract

Botulinum neurotoxins (BoNT) are the most potent toxins in the world. They are produced by a few dozens of strains within several clostridial species. The toxin that they produce can cause botulism, a flaccid paralysis in humans and other animals. With seven established serologically different types and over 40 subtypes, BoNTs are among the most diverse known toxins. The toxin, its structure, its function and its physiological effects on the neural cell and animal hosts along with its diversity have been the subjects of numerous studies. However, many gaps remain in our knowledge about the BoNT toxin and the species that produce them. One of these gaps involves the distribution and extent of variability along the full length of the gene and the protein as well as its domains and subdomains. In this study, we performed an extensive analysis of all of the available 143 unique BoNT-encoding genes and their products, and we investigated their diversity and evolution. Our results indicate that while the nucleotide variability is almost uniformly distributed along the entire length of the gene, the amino acid variability is not. We found that most of the differences were concentrated along the protein’s light chain (LC) domain and especially, the C-terminus of the receptor-binding domain (H_CC). These two regions of the protein are thus identified as the main source of the toxin type differentiation, and consequently, this toxin’s versatility to bind different receptors and their isoforms and act upon different substrates, thus infecting different hosts. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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18 pages, 3572 KiB

Open AccessArticle

Laboratory-Controlled Experiments Reveal Microbial Community Shifts during Sediment Resuspension Events

by Alexis DesRosiers, Nathalie Gassama, Cécile Grosbois and Cassandre Sara Lazar

Genes 2022, 13(8), 1416; https://doi.org/10.3390/genes13081416 - 09 Aug 2022

Viewed by 1338

Abstract

In freshwater ecosystems, dynamic hydraulic events (floods or dam maintenance) lead to sediment resuspension and mixing with waters of different composition. Microbial communities living in the sediments play a major role in these leaching events, contributing to organic matter degradation and the release of trace elements. However, the dynamics of community diversity are seldom studied in the context of ecological studies. Therefore, we carried out laboratory-induced leaching experiments, using sediments from the Villerest dam reservoir (Villerest, France). To assess whole microbial community diversity, we sequenced the archaeal and bacterial 16S rRNA genes using Illumina MiSeq. Our results suggest that the degree of dissolved oxygen found in the water during these resuspension episodes influenced community dynamics, with anoxic waters leading to drastic shifts in sedimentary communities compared to oxic waters. Furthermore, the release of microbial cells from sediments to the water column were more favorable to water colonization when events were caused by oxic waters. Most of the bacteria found in the sediments were chemoorganotrophs and most of the archaea were methanogens. Methylotrophic, as well as archaeal, and bacterial chemoorganotrophs were detected in the leachate samples. These results also show that organic matter degradation occurred, likely participating in carbonate dissolution and the release of trace elements during freshwater resuspension events. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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14 pages, 1508 KiB

Open AccessArticle

Variability in the Pre-Analytical Stages Influences Microbiome Laboratory Analyses

by Aditi Kumar, Kristin Gravdal, Jonathan P. Segal, Helen Steed, Matthew J. Brookes and Hafid O. Al-Hassi

Genes 2022, 13(6), 1069; https://doi.org/10.3390/genes13061069 - 15 Jun 2022

Cited by 1 | Viewed by 1614

Abstract

Introduction: There are numerous confounding variables in the pre-analytical steps in the analysis of gut microbial composition that affect data consistency and reproducibility. This study compared two DNA extraction methods from the same faecal samples to analyse differences in microbial composition. Methods: DNA was extracted from 20 faecal samples using either (A) chemical/enzymatic heat lysis (lysis buffer, proteinase K, 95 °C + 70 °C) or (B) mechanical and chemical/enzymatic heat lysis (bead-beating, lysis buffer, proteinase K, 65 °C). Gut microbiota was mapped through the 16S rRNA gene (V3–V9) using a set of pre-selected DNA probes targeting >300 bacteria on different taxonomic levels. Apart from the pre-analytical DNA extraction technique, all other parameters including microbial analysis remained the same. Bacterial abundance and deviations in the microbiome were compared between the two methods. Results: Significant variation in bacterial abundance was seen between the different DNA extraction techniques, with a higher yield of species noted in the combined mechanical and heat lysis technique (B). The five predominant bacteria seen in both (A) and (B) were Bacteroidota spp. and Prevotella spp. (p = NS), followed by Bacillota (p = 0.005), Lachhnospiraceae (p = 0.0001), Veillonella spp. (p < 0.0001) and Clostridioides (p < 0.0001). Conclusion: As microbial testing becomes more easily and commercially accessible, a unified international consensus for optimal sampling and DNA isolation procedures must be implemented for robustness and reproducibility of the results. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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12 pages, 1401 KiB

Open AccessArticle

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

by Shougang Wang, Xiaoyan Su, Han Cui, Meng Wang, Xiaoli Hu, Wei Ding and Weipeng Zhang

Genes 2022, 13(6), 1050; https://doi.org/10.3390/genes13061050 - 12 Jun 2022

Cited by 7 | Viewed by 3235

Abstract

Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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13 pages, 1689 KiB

Open AccessEditor’s ChoiceArticle

Gut Microbiota as a Potential Predictive Biomarker in Relapsing-Remitting Multiple Sclerosis

by Vicente Navarro-López, María Ángeles Méndez-Miralles, Rosa Vela-Yebra, Ana Fríes-Ramos, Pedro Sánchez-Pellicer, Beatriz Ruzafa-Costas, Eva Núñez-Delegido, Humberto Gómez-Gómez, Sara Chumillas-Lidón, Jose A. Picó-Monllor and Laura Navarro-Moratalla

Genes 2022, 13(5), 930; https://doi.org/10.3390/genes13050930 - 23 May 2022

Cited by 11 | Viewed by 2853

Abstract

Background: The influence of the microbiome on neurological diseases has been studied for years. Recent findings have shown a different composition of gut microbiota detected in patients with multiple sclerosis (MS). The role of this dysbiosis is still unknown. Objective: We analyzed the gut microbiota of 15 patients with active relapsing-remitting multiple sclerosis (RRMS), comparing with diet-matched healthy controls. Method: To determine the composition of the gut microbiota, we performed high-throughput sequencing of the 16S ribosomal RNA gene. The specific amplified sequences were in the V3 and V4 regions of the 16S ribosomal RNA gene. Results: The gut microbiota of RRMS patients differed from healthy controls in the levels of the Lachnospiraceae, Ezakiella, Ruminococcaceae, Hungatella, Roseburia, Clostridium, Shuttleworthia, Poephyromonas, and Bilophila genera. All these genera were included in a logistic regression analysis to determine the sensitivity and the specificity of the test. Finally, the ROC (receiver operating characteristic) and AUC with a 95% CI were calculated and best-matched for Ezakiella (AUC of 75.0 and CI from 60.6 to 89.4) and Bilophila (AUC of 70.2 and CI from 50.1 to 90.4). Conclusions: There is a dysbiosis in the gut microbiota of RRMS patients. An analysis of the components of the microbiota suggests the role of some genera as a predictive factor of RRMS prognosis and diagnosis. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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21 pages, 21079 KiB

Open AccessArticle

Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation

by Isabel Silva, Marta Alves, Catarina Malheiro, Ana Rita R. Silva, Susana Loureiro, Isabel Henriques and M. Nazaret González-Alcaraz

Genes 2022, 13(5), 850; https://doi.org/10.3390/genes13050850 - 10 May 2022

Cited by 6 | Viewed by 2177

Abstract

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15–25 °C or 20–30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community’s physiological profile and the bacterial community’s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20–30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome–invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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14 pages, 2819 KiB

Open AccessArticle

Salinity Gradient Controls Microbial Community Structure and Assembly in Coastal Solar Salterns

by Tianran Song, Qiyun Liang, Zhaozhong Du, Xiaoqun Wang, Guanjun Chen, Zongjun Du and Dashuai Mu

Genes 2022, 13(2), 385; https://doi.org/10.3390/genes13020385 - 21 Feb 2022

Cited by 14 | Viewed by 3033

Abstract

Salinity acts as a critical environmental filter on microbial communities in natural systems, negatively affecting microbial diversity. However, how salinity affects microbial community assembly remains unclear. This study used Wendeng multi-pond saltern as a model to evaluate the prokaryotic community composition and diversity and quantify the relative importance of ecological processes across salinity gradients. The results showed that low-saline salterns (45–80 g/L) exhibited higher bacterial diversity than high-saline salterns (175–265 g/L). The relative abundance of taxa assigned to Halomicrobiaceae, Rhodobacteraceae, Saprospiraceae, and Thiotrichaceae exhibited a hump-shaped dependence on increasing salinity. Salinity and pH were the primary environmental factors that directly or indirectly determined the composition and diversity of prokaryotic communities. Microbial co-occurrence network dynamics were more complex in the sediment than in the water of salterns. An infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis (iCAMP) showed that microbial community assembly in sediment and water differed. Our findings provide more information about microbial community structure and the importance of various ecological processes in controlling microbial community diversity and succession along salinity gradients in water and sediment. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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10 pages, 1742 KiB

Open AccessArticle

Characterization of the Bacterial Community of Rumen in Dairy Cows with Laminitis

by Jian Guo, Ruiying Mu, Shuang Li, Naisheng Zhang, Yunhe Fu and Xiaoyu Hu

Genes 2021, 12(12), 1996; https://doi.org/10.3390/genes12121996 - 16 Dec 2021

Cited by 11 | Viewed by 2777

Abstract

Laminitis is the inflammation of the lamella, and it has caused great economic loss to the dairy industry and attracted wide attention around the world. In recent years, microbiota are considered to play a significant role in various diseases processes. Therefore, our study aimed to explore the characteristics of ruminal microbiota in laminitis cows. The serum of bovines with or without laminitis was collected to detect concentrations of lipopolysaccharide (LPS), lactic acid, and histamine, and ruminal fluid was collected for 16S rDNA sequence analysis. The results showed a significant increase in LPS and lactic acid levels in the laminitis group compared to the control group cows. In addition, a higher abundance of Candidatus Saccharimonas, Saccharofermentans, Erysipelotrichaceae UCG-009 genus, Acetobacter pasteurianus, Clostridium papyrosolvens, Ruminococcaceae bacterium AE2021, Porphyromonas crevioricanis, Pseudomonas boreopolis, Pseudomonas psychrotolerans, Rothia nasimurium, and Rothia pickettii was detected in the rumen fluid of laminitis bovines. In conclusion, this article confirms that there are differences in rumen microbiota between healthy and laminitis bovines. The elevated abundance of bacteria that enrich acid-enhancing metabolites, as well as increase the concentration of lactic acid and LPS, could be harmful factors to bovines and increase the risk of laminitis. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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Review

Jump to: Research

24 pages, 610 KiB

Open AccessReview

How Our Microbiome Influences the Pathogenesis of Alopecia Areata

by Pedro Sánchez-Pellicer, Laura Navarro-Moratalla, Eva Núñez-Delegido, Juan Agüera-Santos and Vicente Navarro-López

Genes 2022, 13(10), 1860; https://doi.org/10.3390/genes13101860 - 14 Oct 2022

Cited by 8 | Viewed by 7633

Abstract

Alopecia areata is a multifactorial autoimmune-based disease with a complex pathogenesis. As in all autoimmune diseases, genetic predisposition is key. The collapse of the immune privilege of the hair follicle leading to scalp loss is a major pathogenic event in alopecia areata. The microbiota considered a bacterial ecosystem located in a specific area of the human body could somehow influence the pathogenesis of alopecia areata, as it occurs in other autoimmune diseases. Moreover, the Next Generation Sequencing of the 16S rRNA bacterial gene and the metagenomic methodology have provided an excellent characterization of the microbiota. The aim of this narrative review is to examine the published literature on the cutaneous and intestinal microbiota in alopecia areata to be able to establish a pathogenic link. In this review, we summarize the influence of the microbiota on the development of alopecia areata. We first introduce the general pathogenic mechanisms that cause alopecia areata to understand the influence that the microbiota may exert and then we summarize the studies that have been carried out on what type of gut and skin microbiota is found in patients with this disease. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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