Pub Date : 2024-01-16DOI: 10.3389/frmbi.2023.1345330
Llilian Arzola-Martínez, Keerthikka Ravi, Gary B. Huffnagle, Nicholas Lukacs, W. Fonseca
Lactobacillus johnsonii is a commensal bacterium that has been isolated from vaginal and gastrointestinal (GI) tracts of vertebrate hosts, including humans, rodents, swine, and poultry. Lactobacillus-based probiotic supplements are popular because of the health advantages they offer. Species such as L. johnsonii are particularly interesting due to their potential health-promoting properties. Here, we reviewed the research on specific strains of L. johnsonii that have been studied in the context of health and disease and delved into the underlying mechanisms that aid in preserving host homeostasis. The utilization of L. johnsonii strains has been widely linked to numerous health benefits in the host. These include pathogen antagonism, control of mucosal and systemic immune responses, reduction of chronic inflammation, modulation of metabolic disorders, and enhanced epithelial barrier. These findings suggest that L. johnsonii plays a critical role in maintaining host homeostasis, highlighting its potential as a probiotic.
{"title":"Lactobacillus johnsonii and host communication: insight into modulatory mechanisms during health and disease","authors":"Llilian Arzola-Martínez, Keerthikka Ravi, Gary B. Huffnagle, Nicholas Lukacs, W. Fonseca","doi":"10.3389/frmbi.2023.1345330","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1345330","url":null,"abstract":"Lactobacillus johnsonii is a commensal bacterium that has been isolated from vaginal and gastrointestinal (GI) tracts of vertebrate hosts, including humans, rodents, swine, and poultry. Lactobacillus-based probiotic supplements are popular because of the health advantages they offer. Species such as L. johnsonii are particularly interesting due to their potential health-promoting properties. Here, we reviewed the research on specific strains of L. johnsonii that have been studied in the context of health and disease and delved into the underlying mechanisms that aid in preserving host homeostasis. The utilization of L. johnsonii strains has been widely linked to numerous health benefits in the host. These include pathogen antagonism, control of mucosal and systemic immune responses, reduction of chronic inflammation, modulation of metabolic disorders, and enhanced epithelial barrier. These findings suggest that L. johnsonii plays a critical role in maintaining host homeostasis, highlighting its potential as a probiotic.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":" 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139619903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-15DOI: 10.3389/frmbi.2023.1279550
H. Peter, G. Michoud, S. Busi, T. Battin
Viruses modulate the diversity and activity of microbial communities. However, little is known about their role for the structure of stream bacterial biofilm communities. Here, we present insights into the diversity and composition of viral communities in various streams draining three proglacial floodplains in Switzerland. Proglacial streams are characterized by extreme environmental conditions, including near-freezing temperatures and ultra-oligotrophy. These conditions select for few but well-adapted bacterial clades, which dominate biofilm communities and occupy niches via microdiversification. We used metagenomic sequencing to reveal a diverse biofilm viral assemblage in these streams. Across the different floodplains and streams, viral community composition was tightly coupled to that of the bacterial hosts, which was underscored by generally high host specificity. Combining predictions of phage-host interactions with auxiliary metabolic genes (AMGs), we identify specific AMGs shared by phages infecting microdiverse clade members. Our work provides a step towards a better understanding of the complex interactions among bacteria and phages in stream biofilm communities in general and streams influenced by glacier meltwaters and characterized by microdiversity in particular.
{"title":"The role of phages for microdiverse bacterial communities in proglacial stream biofilms","authors":"H. Peter, G. Michoud, S. Busi, T. Battin","doi":"10.3389/frmbi.2023.1279550","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1279550","url":null,"abstract":"Viruses modulate the diversity and activity of microbial communities. However, little is known about their role for the structure of stream bacterial biofilm communities. Here, we present insights into the diversity and composition of viral communities in various streams draining three proglacial floodplains in Switzerland. Proglacial streams are characterized by extreme environmental conditions, including near-freezing temperatures and ultra-oligotrophy. These conditions select for few but well-adapted bacterial clades, which dominate biofilm communities and occupy niches via microdiversification. We used metagenomic sequencing to reveal a diverse biofilm viral assemblage in these streams. Across the different floodplains and streams, viral community composition was tightly coupled to that of the bacterial hosts, which was underscored by generally high host specificity. Combining predictions of phage-host interactions with auxiliary metabolic genes (AMGs), we identify specific AMGs shared by phages infecting microdiverse clade members. Our work provides a step towards a better understanding of the complex interactions among bacteria and phages in stream biofilm communities in general and streams influenced by glacier meltwaters and characterized by microdiversity in particular.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"20 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140507364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-11DOI: 10.3389/frmbi.2023.1280809
S. Busi, H. Peter, Jade Brandani, Tyler J. Kohler, S. Fodelianakis, P. Pramateftaki, Massimo Bourquin, G. Michoud, Leïla Ezzat, Stuart Lane, Paul Wilmes, T. Battin
Cross-domain interactions are an integral part of the success of biofilms in natural environments but remain poorly understood. Here, we describe cross-domain interactions in stream biofilms draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterised by multiple environmental gradients and perturbations (e.g., changes in channel geomorphology, discharge) that depend on the time since deglaciation. We evaluate co-occurrence of bacteria and eukaryotic communities along streams and show that key community members have disproportionate effects on the stability of community networks. The topology of the networks, here quantified as the arrangement of the constituent nodes formed by specific taxa, was independent of stream type and their apparent environmental stability. However, network stability against fragmentation was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that bacteria, eukaryotic photoautotrophs, and fungi are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. Key taxa are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.
{"title":"Cross-domain interactions confer stability to benthic biofilms in proglacial streams","authors":"S. Busi, H. Peter, Jade Brandani, Tyler J. Kohler, S. Fodelianakis, P. Pramateftaki, Massimo Bourquin, G. Michoud, Leïla Ezzat, Stuart Lane, Paul Wilmes, T. Battin","doi":"10.3389/frmbi.2023.1280809","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1280809","url":null,"abstract":"Cross-domain interactions are an integral part of the success of biofilms in natural environments but remain poorly understood. Here, we describe cross-domain interactions in stream biofilms draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterised by multiple environmental gradients and perturbations (e.g., changes in channel geomorphology, discharge) that depend on the time since deglaciation. We evaluate co-occurrence of bacteria and eukaryotic communities along streams and show that key community members have disproportionate effects on the stability of community networks. The topology of the networks, here quantified as the arrangement of the constituent nodes formed by specific taxa, was independent of stream type and their apparent environmental stability. However, network stability against fragmentation was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that bacteria, eukaryotic photoautotrophs, and fungi are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. Key taxa are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"42 26","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139533391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-11DOI: 10.3389/frmbi.2023.1310790
Hannah M. Goemann, Danielle E. M. Ulrich, Brent M. Peyton, La Verne Gallegos-Graves, Rebecca C. Mueller
Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.
{"title":"Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome","authors":"Hannah M. Goemann, Danielle E. M. Ulrich, Brent M. Peyton, La Verne Gallegos-Graves, Rebecca C. Mueller","doi":"10.3389/frmbi.2023.1310790","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1310790","url":null,"abstract":"Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":" 48","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139625745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-08DOI: 10.3389/frmbi.2023.1329925
Danny Ionescu, Luca Zoccarato, P. J. Cabello‐Yeves, Y. Tikochinski
Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper “salt-in” and more expensive “salt-out” strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.
{"title":"Extreme fluctuations in ambient salinity select for bacteria with a hybrid “salt-in”/”salt-out” osmoregulation strategy","authors":"Danny Ionescu, Luca Zoccarato, P. J. Cabello‐Yeves, Y. Tikochinski","doi":"10.3389/frmbi.2023.1329925","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1329925","url":null,"abstract":"Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper “salt-in” and more expensive “salt-out” strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"54 27","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139447159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-03DOI: 10.3389/frmbi.2023.1272625
Sen Ma, Yan Zhang, Zidan Li, Ming Guo, Boshuai Liu, Zhichang Wang, Yalei Cui, Chengzhang Wang, Defeng Li, Yinghua Shi
Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4+ and CD8+) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level.
粗饲料质量是影响反刍动物生长性能和饲养成本的一个关键因素；然而，目前仍缺乏对其内在机制的系统研究。在这项研究中，我们考察了饲喂低质或优质饲草的断奶后胡羊的生长性能、肉质、瘤胃发酵参数、瘤胃微生物组和组织甲基组。结果表明，苜蓿干草组（AG）和花生藤组（PG）绵羊的生长性能、屠宰性能和肉质均优于小麦秸秆组（WG）绵羊。与 WG 和 PG 组相比，AG 组绵羊的血清免疫球蛋白（IgA、IgG 和 IgM）含量相对较高，血清炎症因子（TNF-α、IL-1β、IL-6 和 IL-8）含量较低。此外，AG 羊血液中 T 淋巴细胞（CD4+ 和 CD8+）的水平以及 CD4 与 CD8 的比值也明显高于 WG 羊和 PG 羊。WG 羊的瘤胃 NH3-N 浓度最高，而 PG 羊的单个和总短链脂肪酸 (SCFA) 浓度最高。三组绵羊瘤胃乳头的长度、宽度和表面积存在明显差异，其中 PG 组绵羊的瘤胃乳头形态最为发达。主要的瘤胃微生物属包括普雷沃特氏菌 1、Rikenellaceae RC9 肠道组、norank f F082、反刍球菌 1 和反刍球菌 2。某些物种的相对丰度与发酵参数和生长指数呈正或负相关。例如，纤维分解菌反刍球菌科 UGG-001 与 SCFAs（丙酸盐除外）的浓度呈正相关。此外，纤维分解菌（如 Ruminoccus 1）的相对丰度与淀粉降解菌（如 Prevotellaceae）呈负相关。全基因组 DNA 甲基化分析表明，PG 羊和 WG 羊的瘤胃组织占据不同的全局 DNA 甲基化组。启动子甲基化程度不同的基因涉及与瘤胃发育有关的已知通路（如 FoxO 信号通路）和基因本体（Gene Ontology，GO）术语（如解剖结构形态发生）。筛选出两个启动子甲基化过高和过低的候选基因（ACADL 和 ENSOARG00020014533），作为瘤胃发育的潜在调控因子。总之，粗饲料质量通过直接影响瘤胃发酵和微生物组组成，并在表观遗传学水平上间接影响瘤胃发育，从而决定绵羊的生长性能。
{"title":"Roughage quality determines the production performance of post-weaned Hu sheep via altering ruminal fermentation, morphology, microbiota, and the global methylome landscape of the rumen wall","authors":"Sen Ma, Yan Zhang, Zidan Li, Ming Guo, Boshuai Liu, Zhichang Wang, Yalei Cui, Chengzhang Wang, Defeng Li, Yinghua Shi","doi":"10.3389/frmbi.2023.1272625","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1272625","url":null,"abstract":"Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4+ and CD8+) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139451130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fecal microbiota transplantation (FMT) has been tested for the prevention and treatment of various intestinal and extra-intestinal diseases, but its efficacy is not stable, which may be due to the lack of an optimized method for screening high-quality donors. The low efficiency and high cost of donor screening are also obstacles to the clinical application of FMT. In this study, we tested the efficiency of the constitution theory of traditional Chinese medicine (TCM) in screening high-quality FMT donors. College student volunteers were sorted into either the balanced TCM constitution (BC) or unbalanced TCM constitution (UBC) groups, with the latter group comprising eight different constitution types, and the gut microbiota profiles of each UBC were compared with that of BC. Subsequently, the success rates of the qualified donors of BC and UBC volunteers were compared. Finally, the anti-obesity effect of FMT, obtained using the fecal microbiota of BC and UBC donors, was tested on mice with high fat diet-induced obesity. The results showed that the gut microbiota of BC and UBC volunteers were significantly different. There was a higher proportion of qualified FMT donors in the BC volunteer group than in the UBC volunteer group. Moreover, the experiment in mice showed that the fecal microbiota of BC and UBC volunteers conferred different anti-obesity effects. Overall, TCM constitution could be a reference for FMT practice. Our study presents a new idea, namely, using TCM constitution theory to efficiently screen high-quality FMT donors.
粪便微生物群移植（FMT）已被用于预防和治疗各种肠道和肠道外疾病，但其疗效并不稳定，这可能是由于缺乏筛选优质供体的优化方法。供体筛选的低效率和高成本也是 FMT 临床应用的障碍。在本研究中，我们测试了中医体质理论在筛选高质量 FMT 供体中的效率。我们将大学生志愿者分为中医体质平衡组（BC）和中医体质不平衡组（UBC），后者包括八种不同的体质类型，并比较了每种 UBC 与 BC 的肠道微生物群谱。随后，比较了 BC 和 UBC 志愿者合格供体的成功率。最后，利用 BC 和 UBC 捐赠者的粪便微生物群，在高脂饮食诱发肥胖的小鼠身上测试了 FMT 的抗肥胖效果。结果显示，BC 和 UBC 志愿者的肠道微生物群存在显著差异。在 BC 志愿者组中，合格的 FMT 捐赠者比例高于 UBC 志愿者组。此外，小鼠实验表明，BC 和 UBC 志愿者的粪便微生物群具有不同的抗肥胖作用。总之，中医体质可作为 FMT 实践的参考。我们的研究提出了一个新思路，即利用中医体质理论有效筛选高质量的 FMT 供体。
{"title":"Comparison of the gut microbiota of college students with the nine balanced and unbalanced traditional Chinese medicine constitutions and its potential application in fecal microbiota transplantation","authors":"Qinhong Huang, Lihui Yang, Guannan Cai, Yongdie Huang, Shian Zhang, Zhenwei Ye, Jing Yang, Chuhui Gao, Jiaxuan Lai, Lyu Lin, Jihui Wang, Ting Liu","doi":"10.3389/frmbi.2023.1292273","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1292273","url":null,"abstract":"Fecal microbiota transplantation (FMT) has been tested for the prevention and treatment of various intestinal and extra-intestinal diseases, but its efficacy is not stable, which may be due to the lack of an optimized method for screening high-quality donors. The low efficiency and high cost of donor screening are also obstacles to the clinical application of FMT. In this study, we tested the efficiency of the constitution theory of traditional Chinese medicine (TCM) in screening high-quality FMT donors. College student volunteers were sorted into either the balanced TCM constitution (BC) or unbalanced TCM constitution (UBC) groups, with the latter group comprising eight different constitution types, and the gut microbiota profiles of each UBC were compared with that of BC. Subsequently, the success rates of the qualified donors of BC and UBC volunteers were compared. Finally, the anti-obesity effect of FMT, obtained using the fecal microbiota of BC and UBC donors, was tested on mice with high fat diet-induced obesity. The results showed that the gut microbiota of BC and UBC volunteers were significantly different. There was a higher proportion of qualified FMT donors in the BC volunteer group than in the UBC volunteer group. Moreover, the experiment in mice showed that the fecal microbiota of BC and UBC volunteers conferred different anti-obesity effects. Overall, TCM constitution could be a reference for FMT practice. Our study presents a new idea, namely, using TCM constitution theory to efficiently screen high-quality FMT donors.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"26 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139169379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-20DOI: 10.3389/frmbi.2023.1287336
Lin Chen, Haiyan Ding, Xin Chen, Jiaojiao Wang, Yuan Hu, Hongping Chen, You-ping Liu
The plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.In this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.The main microbial taxa in the rhizosphere and root endosphere of D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).This study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.
植物微生物组是植物的第二基因组，对植物的生长和健康非常重要。铁皮石斛是兰科附生草本植物，常附着在树干或岩石上，有不同的栽培模式。对不同栽培模式下的石斛（Dendrobium denneanum Kerr）进行微生物和代谢物研究，可以揭示石斛属植物之间的重要关系、本研究选择了石斛在同一环境中的三种栽培模式：活体树上附生（LT）、石上附生（SE）和盆栽（PO），并采用超高效液相色谱-四极杆飞行时间质谱（UPLC-Q-TOF-MS）对其代谢物进行了测定。D.denneanum根圈和根内圈的主要微生物类群包括属于变形菌门（Proteobacteria）、放线菌门（Actinobacteria）和放线菌门（Actinobacteria）的细菌，以及真菌门（Basidiomycota）和子囊菌门（Ascomycota），它们的丰度在不同的栽培模式下有所不同。土壤特性会影响 D. denneanum 代谢产物和根微生物群的组成，其中土壤全磷（TP）和 pH 值尤其是土壤微生物的重要因素。对根系微生物群落的研究表明，根系内圈真菌与根圈真菌相似，从外部环境到内部结构都有微生物富集。根系微生物群落和代谢物相关性分析表明，根圈微生物以及内生菌和代谢物之间存在显著的相关性。本研究从微生物和代谢物的角度阐明了不同栽培模式对丹顶鹤的影响，并研究了根系微生物对代谢物的影响。研究结果加深了人们对兰科植物根部微生物的认识，为以石斛为代表的石斛属植物的栽培提供了理论依据。
{"title":"Cultivation modes impacting root microbiomes and metabolites in medicinal orchid Dendrobium denneanum","authors":"Lin Chen, Haiyan Ding, Xin Chen, Jiaojiao Wang, Yuan Hu, Hongping Chen, You-ping Liu","doi":"10.3389/frmbi.2023.1287336","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1287336","url":null,"abstract":"The plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.In this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.The main microbial taxa in the rhizosphere and root endosphere of D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).This study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"13 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138955024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-14DOI: 10.3389/frmbi.2023.1270352
Z. G. Griffiths, Andrew D. Putt, J. I. Miller, M. F. Campa, D. Joyner, O. Pelz, Nargiz Garajayeva, M. Ceccopieri, P. Gardinali, Terry C. Hazen
The Caspian Sea is the world’s largest landlocked saline lake which lies between Europe and Asia. This region is particularly known for its large-scale oil reserves, pipelines, and drilling activities, which have contributed to the environmental decline of this lake. In addition to pollution from the petroleum industry, drainage from various river basins brings an influx of residential, industrial, and agricultural effluents that induce eutrophication and hypoxic conditions in deeper, colder waters, creating an oxygen gradient. The temperature and oxygen stratification in this environment has presented a unique opportunity to investigate the potential of the biodegradative processes carried out by the indigenous microbial community. We believe these indigenous microbes possess different metabolic capabilities to degrade oil as they adapted to declining oxygen concentrations and temperatures with increasing depths over a prolonged period. Hence, community structure and composition will vary with depth.Microcosms were set up to observe the indigenous microbial reaction after a 60 ppm native crude oil amendment over 115 days. Surface water microcosms were incubated at 28ºC and aerated while deep water microcosms were incubated at 8ºC under anaerobic conditions. These two environmental conditions represent the temperature and oxygen extremes along the gradient and were selected as we try to simulate the indigenous community’s response to this oil contamination. DNA was extracted and amplified from these microcosms and sequenced. Bioinformatic analysis was performed to track changes in the abundance of taxa present and biodiversity over different time points to show the progression of community structure.All microcosms showed the presence of hydrocarbon-degrading phyla, whose presence is consistent with other reports from oil-enriched environments. However, distinct communities were observed in oxic versus hypoxic microcosms.Orders of Bacteria related to sulfate and nitrogen cycling were found in hypoxic microcosms, indicating a possible mechanism for the anaerobic biodegradation of crude oil. GC-MS analysis of initial and final microcosms also provided evidence of degradation of hydrocarbon fractions in both warm, oxic and cold, hypoxic conditions.
{"title":"Comparing the response of the indigenous microbial community to crude oil amendment in oxic versus hypoxic conditions","authors":"Z. G. Griffiths, Andrew D. Putt, J. I. Miller, M. F. Campa, D. Joyner, O. Pelz, Nargiz Garajayeva, M. Ceccopieri, P. Gardinali, Terry C. Hazen","doi":"10.3389/frmbi.2023.1270352","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1270352","url":null,"abstract":"The Caspian Sea is the world’s largest landlocked saline lake which lies between Europe and Asia. This region is particularly known for its large-scale oil reserves, pipelines, and drilling activities, which have contributed to the environmental decline of this lake. In addition to pollution from the petroleum industry, drainage from various river basins brings an influx of residential, industrial, and agricultural effluents that induce eutrophication and hypoxic conditions in deeper, colder waters, creating an oxygen gradient. The temperature and oxygen stratification in this environment has presented a unique opportunity to investigate the potential of the biodegradative processes carried out by the indigenous microbial community. We believe these indigenous microbes possess different metabolic capabilities to degrade oil as they adapted to declining oxygen concentrations and temperatures with increasing depths over a prolonged period. Hence, community structure and composition will vary with depth.Microcosms were set up to observe the indigenous microbial reaction after a 60 ppm native crude oil amendment over 115 days. Surface water microcosms were incubated at 28ºC and aerated while deep water microcosms were incubated at 8ºC under anaerobic conditions. These two environmental conditions represent the temperature and oxygen extremes along the gradient and were selected as we try to simulate the indigenous community’s response to this oil contamination. DNA was extracted and amplified from these microcosms and sequenced. Bioinformatic analysis was performed to track changes in the abundance of taxa present and biodiversity over different time points to show the progression of community structure.All microcosms showed the presence of hydrocarbon-degrading phyla, whose presence is consistent with other reports from oil-enriched environments. However, distinct communities were observed in oxic versus hypoxic microcosms.Orders of Bacteria related to sulfate and nitrogen cycling were found in hypoxic microcosms, indicating a possible mechanism for the anaerobic biodegradation of crude oil. GC-MS analysis of initial and final microcosms also provided evidence of degradation of hydrocarbon fractions in both warm, oxic and cold, hypoxic conditions.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"10 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138972187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-04DOI: 10.3389/frmbi.2023.1301609
Melanie C. Hay, A. Hinsu, P. Koringa, Ramesh J. Pandit, Po-Yu Liu, M. J. Parekh, S. Jakhesara, Xiaoxai Dai, M. Crotta, Bruno Fosso, G. Limon, Javier Guitian, Fiona M. Tomley, Dong Xia, A. Psifidi, Chaitanya G. Joshi, D. Blake
Identifying farming practices that decrease susceptibility to infectious diseases and optimise food conversion efficiency is valuable for chicken welfare and productivity, the environment, and public health. Enterotypes can be used to define microbial community phenotypes that have differential, potentially significant impacts on gut health. In this study, we delineated enterotypes by analysing the microbiomes of 300 indigenous Kadaknath and 300 commercial Cobb400 broiler chickens raised across 60 farms in western India. Using a compositional data approach, we identified three distinct enterotypes: PA1 (n=290), PA2 (n=142) and PA3 (n=67). PA1 and PA2 clustered more closely with each other than with PA3, however, PA2 had significantly lower alpha diversity than PA1. PA1 had a high Firmicutes: Bacteroides ratio, was dominated by Faecalibacterium and had a higher abundance of Prevotellamassilia than other enterotypes. PA2 was characterised by its low alpha diversity, a high abundance of the common taxa Phascolarctobacterium A and Phocaeicola dorei and a significantly higher Campylobacter abundance than PA1. PA3 had the highest Bacteroidota abundance of the three enterotypes and was defined by high prevalence of lower abundance taxa such as CAG-831 and Mucispirillum schaedleri. Network analysis showed that all enterotypes have different proportions of competing Firmicutes-dominant and Bacteroidota-dominant guilds. Random Forest Modelling using defined farm characteristics was predictive for enterotype. Factors affecting enterotype include whether farms were open, enclosed or caged, the location of farms, whether visitors were allowed inside, the number of people in contact with the chickens, chicken line, the presence of dogs and whether flock thinning took place. This study suggests that enterotypes are influenced by farming practices, hence modification of practices could potentially be used to reduce the burden of zoonotic pathogens such as Campylobacter.
{"title":"Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices","authors":"Melanie C. Hay, A. Hinsu, P. Koringa, Ramesh J. Pandit, Po-Yu Liu, M. J. Parekh, S. Jakhesara, Xiaoxai Dai, M. Crotta, Bruno Fosso, G. Limon, Javier Guitian, Fiona M. Tomley, Dong Xia, A. Psifidi, Chaitanya G. Joshi, D. Blake","doi":"10.3389/frmbi.2023.1301609","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1301609","url":null,"abstract":"Identifying farming practices that decrease susceptibility to infectious diseases and optimise food conversion efficiency is valuable for chicken welfare and productivity, the environment, and public health. Enterotypes can be used to define microbial community phenotypes that have differential, potentially significant impacts on gut health. In this study, we delineated enterotypes by analysing the microbiomes of 300 indigenous Kadaknath and 300 commercial Cobb400 broiler chickens raised across 60 farms in western India. Using a compositional data approach, we identified three distinct enterotypes: PA1 (n=290), PA2 (n=142) and PA3 (n=67). PA1 and PA2 clustered more closely with each other than with PA3, however, PA2 had significantly lower alpha diversity than PA1. PA1 had a high Firmicutes: Bacteroides ratio, was dominated by Faecalibacterium and had a higher abundance of Prevotellamassilia than other enterotypes. PA2 was characterised by its low alpha diversity, a high abundance of the common taxa Phascolarctobacterium A and Phocaeicola dorei and a significantly higher Campylobacter abundance than PA1. PA3 had the highest Bacteroidota abundance of the three enterotypes and was defined by high prevalence of lower abundance taxa such as CAG-831 and Mucispirillum schaedleri. Network analysis showed that all enterotypes have different proportions of competing Firmicutes-dominant and Bacteroidota-dominant guilds. Random Forest Modelling using defined farm characteristics was predictive for enterotype. Factors affecting enterotype include whether farms were open, enclosed or caged, the location of farms, whether visitors were allowed inside, the number of people in contact with the chickens, chicken line, the presence of dogs and whether flock thinning took place. This study suggests that enterotypes are influenced by farming practices, hence modification of practices could potentially be used to reduce the burden of zoonotic pathogens such as Campylobacter.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"30 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138604019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：