Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.
{"title":"Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities.","authors":"Tian You, Qiumei Liu, Meng Chen, Siyu Tang, Lijun Ou, Dejun Li","doi":"10.3390/microorganisms13010148","DOIUrl":"10.3390/microorganisms13010148","url":null,"abstract":"<p><p>Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as <i>Scedosporium</i>, <i>Sordariomycetes</i>, <i>Pseudarthrobacter</i>, <i>norankSBR1031</i>, and <i>norankA4b</i> significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like <i>Sordariomycetes</i> and <i>Pseudarthrobacter</i>, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.3390/microorganisms13010153
Huawei Wang, Jinxing He
As the mobile cassette carrier of the methicillin resistance gene mecA that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome mec (SCCmec)-and in particular, the composition of mecA and SCCmec-have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCCmec. Herein, the cassette chromosome recombinase genes ccrAB/C, as essential components of SCCmec, were employed to explore the evolution of SCCmec. This work established the basic taxonomy of 33 staphylococci species. The CUB of mecA, ccrAB/C of 12 SCCmec types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of ccrAB/C was observed via SCCmec typing on a temporal and geographical scale; and the duplicate appearance of ccrAB/C was illustrated by comparing SCCmec compositions. The results highlighted a deviation in the CUB of mecA and ccrAB/C, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of ccrAB/C as representative of SCCmec. Importantly, the phylogenetic relationship of ccrAB/C did not exhibit centralization over time; instead, similarly to mecA, ccrAB/C with similar identities had close clades across decades and geographical limits and different SCCmec types, which enabled us to discriminate SCCmec based on the sequence identity of ccrAB/C. In addition, the duplicate appearance of ccrAB/C and fixed composition of the ccrAB/C complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCCmec.
{"title":"In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i>.","authors":"Huawei Wang, Jinxing He","doi":"10.3390/microorganisms13010153","DOIUrl":"10.3390/microorganisms13010153","url":null,"abstract":"<p><p>As the mobile cassette carrier of the methicillin resistance gene <i>mecA</i> that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>)-and in particular, the composition of <i>mecA</i> and SCC<i>mec</i>-have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCC<i>mec</i>. Herein, the cassette chromosome recombinase genes <i>ccrAB/C</i>, as essential components of SCC<i>mec</i>, were employed to explore the evolution of SCC<i>mec</i>. This work established the basic taxonomy of 33 staphylococci species. The CUB of <i>mecA</i>, <i>ccrAB/C</i> of 12 SCC<i>mec</i> types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of <i>ccrAB/C</i> was observed via SCC<i>mec</i> typing on a temporal and geographical scale; and the duplicate appearance of <i>ccrAB/C</i> was illustrated by comparing SCC<i>mec</i> compositions. The results highlighted a deviation in the CUB of <i>mecA</i> and <i>ccrAB/C</i>, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of <i>ccrAB/C</i> as representative of SCC<i>mec</i>. Importantly, the phylogenetic relationship of <i>ccrAB/C</i> did not exhibit centralization over time; instead, similarly to <i>mecA</i>, <i>ccrAB/C</i> with similar identities had close clades across decades and geographical limits and different SCC<i>mec</i> types, which enabled us to discriminate SCC<i>mec</i> based on the sequence identity of <i>ccrAB/C</i>. In addition, the duplicate appearance of <i>ccrAB/C</i> and fixed composition of the <i>ccrAB/C</i> complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCC<i>mec</i>.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rotavirus A (RVA) is the primary enteric pathogen of humans and many other species. However, RVA interspecies transmission remains poorly understood. In this study, we conducted a comprehensive screening and genotyping analysis of RVA in 1706 wild animal samples collected from various regions within Yunnan Province, China. A total of 24 samples, originating from wild boars, rodents, bats, and birds tested positive for RVA. Next generation sequencing and phylogenetic analyses revealed a high degree of genetic diversity and reassortment, particularly for VP4 and VP7. Strains isolated from wild boars and rodents exhibited gene segments with high similarity to those found in humans and other mammalian RVA strains, indicating that RVA may undergo interspecies transmission and reassortment, resulting in novel strains with potential risks for human infection. This study provides critical data for understanding the transmission mechanisms and the RVA host range, and highlights the pivotal role of wildlife in viral evolution and dissemination. These findings have significant implications for public health policies and emphasize the need for enhanced surveillance to prevent interspecies RVA transmission.
{"title":"Diversity and Potential Cross-Species Transmission of Rotavirus A in Wild Animals in Yunnan, China.","authors":"Xiang Le, Yinzhu Tao, Binghui Wang, Yutong Hou, Yuting Ning, Junjie Hou, Ruimei Wang, Qian Li, Xueshan Xia","doi":"10.3390/microorganisms13010145","DOIUrl":"10.3390/microorganisms13010145","url":null,"abstract":"<p><p>Rotavirus A (RVA) is the primary enteric pathogen of humans and many other species. However, RVA interspecies transmission remains poorly understood. In this study, we conducted a comprehensive screening and genotyping analysis of RVA in 1706 wild animal samples collected from various regions within Yunnan Province, China. A total of 24 samples, originating from wild boars, rodents, bats, and birds tested positive for RVA. Next generation sequencing and phylogenetic analyses revealed a high degree of genetic diversity and reassortment, particularly for VP4 and VP7. Strains isolated from wild boars and rodents exhibited gene segments with high similarity to those found in humans and other mammalian RVA strains, indicating that RVA may undergo interspecies transmission and reassortment, resulting in novel strains with potential risks for human infection. This study provides critical data for understanding the transmission mechanisms and the RVA host range, and highlights the pivotal role of wildlife in viral evolution and dissemination. These findings have significant implications for public health policies and emphasize the need for enhanced surveillance to prevent interspecies RVA transmission.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.3390/microorganisms13010143
Shaotang Ye, Zhen Wang, Aolei Chen, Ying Chen, Gaoming Lou, Qingmei Xie, Gang Lu, Shoujun Li
Developing novel antiviral drugs has always been a significant forefront in biological medicine research. Antiviral drugs can be extracted, purified, and synthesized from various biological sources and by different methods. However, they are less explored in veterinary medicine for animal viruses. This research primarily selected feline calicivirus (FCV) to screen the novel antiviral drug against animal viruses. A preliminary screening from a natural product library was conducted, with subsequent assessments to ascertain their toxicity levels and antiviral capabilities. The results showed that decitabine and alprostadil were effective in reducing FCV replication. The decitabine (5-aza-2'-deoxycytidine) was selected for antiviral mechanism investigation. Decitabine has been proven to modulate gene expression through its demethylating effect. Thus, we carried out further experiments and found that decitabine inhibited the FCV by enhancing the transcription of the feline Retinoic acid-inducible gene I (RIG-I) gene. Moreover, we also validated the same antiviral effect and mechanism of decitabine against the canine influenza virus (CIV). In summary, this study unveils the antiviral role of decitabine against FCV and CIV and provides evidence and novel insights into the demethylation drug-mediated antiviral effect for animal RNA viruses.
{"title":"Decitabine Increases the Transcription of <i>RIG-I</i> Gene to Suppress the Replication of Feline Calicivirus and Canine Influenza Virus.","authors":"Shaotang Ye, Zhen Wang, Aolei Chen, Ying Chen, Gaoming Lou, Qingmei Xie, Gang Lu, Shoujun Li","doi":"10.3390/microorganisms13010143","DOIUrl":"10.3390/microorganisms13010143","url":null,"abstract":"<p><p>Developing novel antiviral drugs has always been a significant forefront in biological medicine research. Antiviral drugs can be extracted, purified, and synthesized from various biological sources and by different methods. However, they are less explored in veterinary medicine for animal viruses. This research primarily selected feline calicivirus (FCV) to screen the novel antiviral drug against animal viruses. A preliminary screening from a natural product library was conducted, with subsequent assessments to ascertain their toxicity levels and antiviral capabilities. The results showed that decitabine and alprostadil were effective in reducing FCV replication. The decitabine (5-aza-2'-deoxycytidine) was selected for antiviral mechanism investigation. Decitabine has been proven to modulate gene expression through its demethylating effect. Thus, we carried out further experiments and found that decitabine inhibited the FCV by enhancing the transcription of the feline <i>Retinoic acid-inducible gene I (RIG-I)</i> gene. Moreover, we also validated the same antiviral effect and mechanism of decitabine against the canine influenza virus (CIV). In summary, this study unveils the antiviral role of decitabine against FCV and CIV and provides evidence and novel insights into the demethylation drug-mediated antiviral effect for animal RNA viruses.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.3390/microorganisms13010146
Binoop Mohan, Chandrima Karthik, Doni Thingujam, Karolina M Pajerowska-Mukhtar, Vinoy Thomas, M Shahid Mukhtar
Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of plant microbiomes or the concentration of plant metabolites. We delve into the mechanisms by which plasma can regulate microbial communities, enhance antimicrobial activity, and recruit beneficial microbes to mitigate stress. Furthermore, we discuss the optimization of plasma parameters for effective microbiome interaction and the role of plasmids in plant-microbe interactions. By characterizing plasmidome responses to plasma exposure and investigating transcriptional and metabolomic shifts, we provide insights into the potential of plasma as a tool for engineering beneficial plant-microbe interactions. The review presented herein demonstrates that plasma treatment induces substantial changes in both microbial community composition and metabolite levels, thereby refuting our initial hypothesis. Finally, we integrate plasmidome, transcriptome, and metabolome data to develop a comprehensive understanding of plasma's effects on plant biology and explore future perspectives for agricultural applications.
{"title":"Plasma Optimization as a Novel Tool to Explore Plant-Microbe Interactions in Climate Smart Agriculture.","authors":"Binoop Mohan, Chandrima Karthik, Doni Thingujam, Karolina M Pajerowska-Mukhtar, Vinoy Thomas, M Shahid Mukhtar","doi":"10.3390/microorganisms13010146","DOIUrl":"10.3390/microorganisms13010146","url":null,"abstract":"<p><p>Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of plant microbiomes or the concentration of plant metabolites. We delve into the mechanisms by which plasma can regulate microbial communities, enhance antimicrobial activity, and recruit beneficial microbes to mitigate stress. Furthermore, we discuss the optimization of plasma parameters for effective microbiome interaction and the role of plasmids in plant-microbe interactions. By characterizing plasmidome responses to plasma exposure and investigating transcriptional and metabolomic shifts, we provide insights into the potential of plasma as a tool for engineering beneficial plant-microbe interactions. The review presented herein demonstrates that plasma treatment induces substantial changes in both microbial community composition and metabolite levels, thereby refuting our initial hypothesis. Finally, we integrate plasmidome, transcriptome, and metabolome data to develop a comprehensive understanding of plasma's effects on plant biology and explore future perspectives for agricultural applications.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Arbuscular mycorrhizal fungi (AMF) can preferentially absorb the released ammonium (NH4+) over nitrate (NO3-) during litter decomposition. However, the impact of AMF's absorption of NH4+ on litter nitrogen (N) decomposition is still unclear. In this study, we investigated the effects of AMF uptake for NH4+ on litter N metabolic characteristics by enriching NH4+ via AMF suppression and nitrification inhibition in a subtropical Cinnamomum camphora forest. The results showed that AMF suppression and nitrification inhibition significantly decelerated litter decomposition in the early stage due to the repression of NH4+ in extracellular enzyme activity. In the late stage, when soil NH4+ content was low, in contrast, they promoted litter decomposition by increasing the extracellular enzyme activities. Nitrification inhibition mainly promoted the utilization of plant-derived N by promoting the degradation of the amide I, amide II, and III bands by increasing protease activity, and it promoted ammonification by increasing urease activities, whereas it reduced the utilization of microbial-derived N by decreasing chitinase activity. On the contrary, AMF suppression, which significantly reduced the ammonification rate and increased the nitrification rate, only facilitated the degradation of the amide II band. Moreover, it intensified the microbial-derived N decomposition by increasing chitinase activity. The degradation of the amide I and II bands still relied on the priming effects of AMF on soil saprotrophs. This was likely driven by AMF-mediated phosphorus (P) mineralization. Nutrient acquiring, especially P by phosphatase, were the main factors in predicting litter decomposition and protein degradation. Thus, AMF could relieve the end-product repression of locally enriched NH4+ in extracellular enzyme activity and promote early-stage litter decomposition. However, the promotive effects of AMF on litter protein degradation and NH4+ release rely on P mineralization. Our results demonstrated that AMF could alleviate the N limitation for net primary production via accelerating litter N decomposition and reducing N loss. Moreover, they could restrict the decomposition of recalcitrant components by competing with saprotrophs for nutrients. Both pathways will contribute to C sequestration in forest ecosystems, which advances our understanding of AMF's contribution to nutrient cycling and ecosystem processes in subtropical forests.
{"title":"Influence of Arbuscular Mycorrhizal Fungi on Nitrogen Dynamics During <i>Cinnamomum camphora</i> Litter Decomposition.","authors":"Yuehong Gao, Xiaoyu Long, Yiqi Liao, Yonghui Lin, Zaihua He, Qin Kong, Xiangshi Kong, Xingbing He","doi":"10.3390/microorganisms13010151","DOIUrl":"10.3390/microorganisms13010151","url":null,"abstract":"<p><p>Arbuscular mycorrhizal fungi (AMF) can preferentially absorb the released ammonium (NH<sub>4</sub><sup>+</sup>) over nitrate (NO<sub>3</sub><sup>-</sup>) during litter decomposition. However, the impact of AMF's absorption of NH<sub>4</sub><sup>+</sup> on litter nitrogen (N) decomposition is still unclear. In this study, we investigated the effects of AMF uptake for NH<sub>4</sub><sup>+</sup> on litter N metabolic characteristics by enriching NH<sub>4</sub><sup>+</sup> via AMF suppression and nitrification inhibition in a subtropical <i>Cinnamomum camphora</i> forest. The results showed that AMF suppression and nitrification inhibition significantly decelerated litter decomposition in the early stage due to the repression of NH<sub>4</sub><sup>+</sup> in extracellular enzyme activity. In the late stage, when soil NH<sub>4</sub><sup>+</sup> content was low, in contrast, they promoted litter decomposition by increasing the extracellular enzyme activities. Nitrification inhibition mainly promoted the utilization of plant-derived N by promoting the degradation of the amide I, amide II, and III bands by increasing protease activity, and it promoted ammonification by increasing urease activities, whereas it reduced the utilization of microbial-derived N by decreasing chitinase activity. On the contrary, AMF suppression, which significantly reduced the ammonification rate and increased the nitrification rate, only facilitated the degradation of the amide II band. Moreover, it intensified the microbial-derived N decomposition by increasing chitinase activity. The degradation of the amide I and II bands still relied on the priming effects of AMF on soil saprotrophs. This was likely driven by AMF-mediated phosphorus (P) mineralization. Nutrient acquiring, especially P by phosphatase, were the main factors in predicting litter decomposition and protein degradation. Thus, AMF could relieve the end-product repression of locally enriched NH<sub>4</sub><sup>+</sup> in extracellular enzyme activity and promote early-stage litter decomposition. However, the promotive effects of AMF on litter protein degradation and NH<sub>4</sub><sup>+</sup> release rely on P mineralization. Our results demonstrated that AMF could alleviate the N limitation for net primary production via accelerating litter N decomposition and reducing N loss. Moreover, they could restrict the decomposition of recalcitrant components by competing with saprotrophs for nutrients. Both pathways will contribute to C sequestration in forest ecosystems, which advances our understanding of AMF's contribution to nutrient cycling and ecosystem processes in subtropical forests.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11768061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lactic acid Bacteria (LAB) convert tryptophan to indole derivatives and induce protective IL-22 production in vivo. However, differences in metabolizing capabilities among LAB species have not been widely investigated. In the present study, we compared the capabilities of 186 LAB strains to produce four kinds of indole derivatives, including indole-3-carboxaldehyde (IAId), indole-3-lactic acid (ILA), indole-3-propanoic acid (IPA), and indole-3-acetic acid (IAA). These strains were isolated from fermented foods, dairy products, and the feces of healthy individuals, as well as from fish and shrimp from Shanxi and Jiangsu provinces. They represent 15 genera, including Bifidobacterium, Enterococcus, Lacticaseibacillus, Lactiplantibacillus, Lactobacillus, Lactococcus, Limosilactobacillus, Pediococcus, Streptococcus, Weissella, Latilactobacillus, Levilactobacillus, Ligilactobacillus, and Loigolactobacillus. The results indicate widespread IAId-producing capabilities in LAB strains, with positive rates of approximately 90% (106/117) and 100% (69/69) among strains from Shanxi and Jiangsu provinces, respectively. The concentrations of IAId ranged from 72.42 ng/mL to 423.14 ng/mL in all positive strains from Shanxi Province and from 169.39 ng/mL to 503.51 ng/mL in strains from Jiangsu Province. Intriguingly, we also observed specific ILA-producing capabilities in Lactiplantibacillus strains, with positive rates of 55.17% (16/29) and 80.95% (17/21) among strains isolated from Shanxi and Jiangsu provinces, respectively. The overall detection rates of ILA among all tested strains (including both Lactiplantibacillus and other genus strains) were 17.9% (21/117) and 26.1% (18/69). The concentrations of ILA in positive strains ranged from 12.22 ng/mL to 101.86 ng/mL and from 5.75 ng/mL to 62.96 ng/mL from Shanxi and Jiangsu provinces, respectively. IPA and IAA were not detected in any strains. Finally, these indole derivative-producing capabilities were not related to their geographical origins or isolation sources. The current study provides insights into the species- or genus-dependent capabilities for metabolizing indole derivatives. Defining the specific roles of LAB in indole derivative metabolism will uncover the exact physiological mechanisms and be helpful for functional strain screening.
{"title":"Evaluation of In Vitro Production Capabilities of Indole Derivatives by Lactic Acid Bacteria.","authors":"Bingyang Ma, Yan Zhao, Liping Liu, Jianguo Xu, Qingping Hu, Saisai Feng, Liangliang Zhang","doi":"10.3390/microorganisms13010150","DOIUrl":"10.3390/microorganisms13010150","url":null,"abstract":"<p><p>Lactic acid Bacteria (LAB) convert tryptophan to indole derivatives and induce protective IL-22 production in vivo. However, differences in metabolizing capabilities among LAB species have not been widely investigated. In the present study, we compared the capabilities of 186 LAB strains to produce four kinds of indole derivatives, including indole-3-carboxaldehyde (IAId), indole-3-lactic acid (ILA), indole-3-propanoic acid (IPA), and indole-3-acetic acid (IAA). These strains were isolated from fermented foods, dairy products, and the feces of healthy individuals, as well as from fish and shrimp from Shanxi and Jiangsu provinces. They represent 15 genera, including <i>Bifidobacterium</i>, <i>Enterococcus</i>, <i>Lacticaseibacillus</i>, <i>Lactiplantibacillus</i>, <i>Lactobacillus</i>, <i>Lactococcus</i>, <i>Limosilactobacillus</i>, <i>Pediococcus</i>, <i>Streptococcus</i>, <i>Weissella</i>, <i>Latilactobacillus</i>, <i>Levilactobacillus</i>, <i>Ligilactobacillus</i>, and <i>Loigolactobacillus</i>. The results indicate widespread IAId-producing capabilities in LAB strains, with positive rates of approximately 90% (106/117) and 100% (69/69) among strains from Shanxi and Jiangsu provinces, respectively. The concentrations of IAId ranged from 72.42 ng/mL to 423.14 ng/mL in all positive strains from Shanxi Province and from 169.39 ng/mL to 503.51 ng/mL in strains from Jiangsu Province. Intriguingly, we also observed specific ILA-producing capabilities in <i>Lactiplantibacillus</i> strains, with positive rates of 55.17% (16/29) and 80.95% (17/21) among strains isolated from Shanxi and Jiangsu provinces, respectively. The overall detection rates of ILA among all tested strains (including both <i>Lactiplantibacillus</i> and other genus strains) were 17.9% (21/117) and 26.1% (18/69). The concentrations of ILA in positive strains ranged from 12.22 ng/mL to 101.86 ng/mL and from 5.75 ng/mL to 62.96 ng/mL from Shanxi and Jiangsu provinces, respectively. IPA and IAA were not detected in any strains. Finally, these indole derivative-producing capabilities were not related to their geographical origins or isolation sources. The current study provides insights into the species- or genus-dependent capabilities for metabolizing indole derivatives. Defining the specific roles of LAB in indole derivative metabolism will uncover the exact physiological mechanisms and be helpful for functional strain screening.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.3390/microorganisms13010154
Bademu Qiqige, Jingjing Liu, Ming Li, Xiaosheng Hu, Weiwei Guo, Ping Wang, Yi Ding, Qiuying Zhi, Yuxuan Wu, Xiao Guan, Junsheng Li
The soil microbiome plays an important role in wetland ecosystem services and functions. However, the impact of soil hydrological conditions on wetland microorganisms is not well understood. This study investigated the effects of wetted state (WS); wetting-drying state (WDS); and dried state (DS) on the diversity of soil bacteria, fungi, and archaea. The Shannon index of bacterial diversity was not significantly different in various flooding conditions (p > 0.05), however, fungal diversity and archaeal communities were significantly different in different flooding conditions (p < 0.05). Significant differences were found in the beta diversity of bacterial, fungal, and archaeal communities (p < 0.05). Additionally, the composition of bacteria, fungi, and archaea varied. Bacteria were predominantly composed of Proteobacteria and Actinobacteria, fungi mainly consisted of Ascomycota and Mucoromycota, and archaea were primarily represented by Crenarchaeota and Euryarchaeota. Bacteria exhibited correlations with vegetation coverage, fungi with plant diversity, and archaea with aboveground vegetation biomass. The pH influenced bacterial and archaeal communities, while soil bulk density, moisture, soil carbon, soil nitrogen, and plant community diversity impacted fungal communities. This study provides a scientific basis for understanding the effects of different hydrological conditions on microbial communities in the Huihe Nature Reserve; highlighting their relationship with vegetation and soil properties, and offers insights for the ecological protection of the Huihe wetland.
{"title":"Different Flooding Conditions Affected Microbial Diversity in Riparian Zone of Huihe Wetland.","authors":"Bademu Qiqige, Jingjing Liu, Ming Li, Xiaosheng Hu, Weiwei Guo, Ping Wang, Yi Ding, Qiuying Zhi, Yuxuan Wu, Xiao Guan, Junsheng Li","doi":"10.3390/microorganisms13010154","DOIUrl":"10.3390/microorganisms13010154","url":null,"abstract":"<p><p>The soil microbiome plays an important role in wetland ecosystem services and functions. However, the impact of soil hydrological conditions on wetland microorganisms is not well understood. This study investigated the effects of wetted state (WS); wetting-drying state (WDS); and dried state (DS) on the diversity of soil bacteria, fungi, and archaea. The Shannon index of bacterial diversity was not significantly different in various flooding conditions (<i>p</i> > 0.05), however, fungal diversity and archaeal communities were significantly different in different flooding conditions (<i>p</i> < 0.05). Significant differences were found in the beta diversity of bacterial, fungal, and archaeal communities (<i>p</i> < 0.05). Additionally, the composition of bacteria, fungi, and archaea varied. Bacteria were predominantly composed of <i>Proteobacteria</i> and <i>Actinobacteria</i>, fungi mainly consisted of <i>Ascomycota</i> and <i>Mucoromycota</i>, and archaea were primarily represented by <i>Crenarchaeota</i> and <i>Euryarchaeota</i>. Bacteria exhibited correlations with vegetation coverage, fungi with plant diversity, and archaea with aboveground vegetation biomass. The pH influenced bacterial and archaeal communities, while soil bulk density, moisture, soil carbon, soil nitrogen, and plant community diversity impacted fungal communities. This study provides a scientific basis for understanding the effects of different hydrological conditions on microbial communities in the Huihe Nature Reserve; highlighting their relationship with vegetation and soil properties, and offers insights for the ecological protection of the Huihe wetland.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.3390/microorganisms13010144
Xuan Yan, Xinyu Zhang, Wei Song, Tangkai Qi, Zhenyan Wang, Yang Tang, Jianjun Sun, Shuibao Xu, Junyang Yang, Jiangrong Wang, Jun Chen, Renfang Zhang, Li Liu, Yinzhong Shen
The underlying mechanisms and diagnostic biomarkers for the progress of COVID-19 in HIV patients have not been fully elucidated. In this study, the aim is to analyze the metabolomic profiles of HIV/AIDS patients co-infected with SARS-CoV-2 and to identify biomarkers indicative of co-infection. In this study, we conducted a retrospective cohort analysis of peripheral blood samples collected from 30 HIV/AIDS patients co-infected with SARS-CoV-2 (pc group) and 30 patients without SARS-CoV-2 (nc group). In this study, through non-targeted metabolomics and lipidomics analysis, 77 differential metabolites were identified in the plasma of patients co-infected with HIV and SARS-CoV-2 compared to the nc group, with vitamin K1 emerging as a significant feature. Moreover, the plasma of the pc group showed disturbances in lipid metabolism, with elevated triglycerides (TG) and phosphatidylcholine (PC) and decreased phosphatidylglycerol (PG) compared to the control group. Vitamin K1 may be a biomarker for SARS-CoV-2 in HIV/AIDS patients, and changes in the levels of TG, PC, and PG molecules appear to be the main features following HIV co-infection with COVID-19. The emphasis in our study is on the power of using comprehensive metabolomics (lipidomics) approaches to identify metabolic biomarkers and potential mechanisms of COVID-19 in HIV/AIDS patients.
{"title":"Metabolomic Profiling Reveals Potential Biomarkers and Prominent Features in HIV/AIDS Patients Co-Infected with SARS-CoV-2.","authors":"Xuan Yan, Xinyu Zhang, Wei Song, Tangkai Qi, Zhenyan Wang, Yang Tang, Jianjun Sun, Shuibao Xu, Junyang Yang, Jiangrong Wang, Jun Chen, Renfang Zhang, Li Liu, Yinzhong Shen","doi":"10.3390/microorganisms13010144","DOIUrl":"10.3390/microorganisms13010144","url":null,"abstract":"<p><p>The underlying mechanisms and diagnostic biomarkers for the progress of COVID-19 in HIV patients have not been fully elucidated. In this study, the aim is to analyze the metabolomic profiles of HIV/AIDS patients co-infected with SARS-CoV-2 and to identify biomarkers indicative of co-infection. In this study, we conducted a retrospective cohort analysis of peripheral blood samples collected from 30 HIV/AIDS patients co-infected with SARS-CoV-2 (pc group) and 30 patients without SARS-CoV-2 (nc group). In this study, through non-targeted metabolomics and lipidomics analysis, 77 differential metabolites were identified in the plasma of patients co-infected with HIV and SARS-CoV-2 compared to the nc group, with vitamin K1 emerging as a significant feature. Moreover, the plasma of the pc group showed disturbances in lipid metabolism, with elevated triglycerides (TG) and phosphatidylcholine (PC) and decreased phosphatidylglycerol (PG) compared to the control group. Vitamin K1 may be a biomarker for SARS-CoV-2 in HIV/AIDS patients, and changes in the levels of TG, PC, and PG molecules appear to be the main features following HIV co-infection with COVID-19. The emphasis in our study is on the power of using comprehensive metabolomics (lipidomics) approaches to identify metabolic biomarkers and potential mechanisms of COVID-19 in HIV/AIDS patients.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.3390/microorganisms13010147
Kristina Magoutas, Sebastian Leathersich, Roger Hart, Demelza Ireland, Melanie Walls, Matthew Payne
The prevalence of infertility is increasing worldwide; poor nutrition, increased sedentary lifestyles, obesity, stress, endocrine-disrupting chemicals, and advanced age of childbearing may contribute to the disruption of ovulation and influence oocyte and sperm quality and overall reproductive health. Historically, infertility has been primarily attributed to female factors, neglecting the importance of male fertility; this has resulted in an incomplete understanding of reproductive health. Male factors account for 40-50% of infertility cases. In half of these cases, the proximal cause for male infertility is unknown. Sperm contributes half of the nuclear DNA to the embryo, and its quality is known to impact fertilisation rates, embryo quality, pregnancy rates, risk of spontaneous miscarriage, de novo autosomal-dominant conditions, psychiatric and neurodevelopment conditions, and childhood diseases. Recent studies have suggested that both the microenvironment of the testes and diet quality may play an important role in fertility; however, there is limited research on the combination of these factors. This review summarises current known causes of male infertility and then focuses on the potential roles for diet and the seminal microbiome. Future research in this area will inform dietary interventions and health advice for men with poor semen quality, potentially alleviating the need for costly and invasive assisted reproduction treatments and allowing men to take an active role in the fertility conversation which has historically focussed on women individually.
{"title":"Lower Semen Quality Among Men in the Modern Era-Is There a Role for Diet and the Microbiome?","authors":"Kristina Magoutas, Sebastian Leathersich, Roger Hart, Demelza Ireland, Melanie Walls, Matthew Payne","doi":"10.3390/microorganisms13010147","DOIUrl":"10.3390/microorganisms13010147","url":null,"abstract":"<p><p>The prevalence of infertility is increasing worldwide; poor nutrition, increased sedentary lifestyles, obesity, stress, endocrine-disrupting chemicals, and advanced age of childbearing may contribute to the disruption of ovulation and influence oocyte and sperm quality and overall reproductive health. Historically, infertility has been primarily attributed to female factors, neglecting the importance of male fertility; this has resulted in an incomplete understanding of reproductive health. Male factors account for 40-50% of infertility cases. In half of these cases, the proximal cause for male infertility is unknown. Sperm contributes half of the nuclear DNA to the embryo, and its quality is known to impact fertilisation rates, embryo quality, pregnancy rates, risk of spontaneous miscarriage, de novo autosomal-dominant conditions, psychiatric and neurodevelopment conditions, and childhood diseases. Recent studies have suggested that both the microenvironment of the testes and diet quality may play an important role in fertility; however, there is limited research on the combination of these factors. This review summarises current known causes of male infertility and then focuses on the potential roles for diet and the seminal microbiome. Future research in this area will inform dietary interventions and health advice for men with poor semen quality, potentially alleviating the need for costly and invasive assisted reproduction treatments and allowing men to take an active role in the fertility conversation which has historically focussed on women individually.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11768045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}