Frontiers in Microbiology最新文献

{"title":"Adaptation of rhizobacterial and endophytic communities in <i>Citrus Grandis Exocarpium</i> to long-term organic and chemical fertilization.","authors":"Deyang Zhou, Kaiqing Yang, Yinhui Zhang, Cancan Liu, Ye He, Jialin Tan, Zhepu Ruan, Rongliang Qiu","doi":"10.3389/fmicb.2024.1461821","DOIUrl":"10.3389/fmicb.2024.1461821","url":null,"abstract":"<p><strong>Introduction: </strong>Organic fertilizers (OF) are crucial for enhancing soil quality and fostering plant growth, offering a more eco-friendly and enduring solution compared to chemical fertilizers (CF). However, few studies have systematically analyzed the effects of OF/CF on root microbiome of medicinal plants, especially in combination with active ingredients.</p><p><strong>Methods: </strong>In this study, we investigated the composition and function of bacteria and fungi in the rhizosphere or within the root of traditional Chinese medicinal plants, <i>Citri Grandis Exocarpium</i> (Huajuhong), which were treated with OF or CF over 1, 3, and 5 years (starting from 2018). Additionally, we conducted metabolome analysis to evaluate the effects of different fertilizers on the medicinal properties of Huajuhong.</p><p><strong>Results: </strong>The results indicated that extended fertilization could enhance the microbial population and function in plant roots. Notably, OF demonstrated a stronger influence on bacteria, whereas CF enhanced the cohesion of fungal networks and the number of fungal functional enzymes, and even potentially reduced the proliferation of harmful rhizosphere pathogens. By adopting distancebased redundancy analysis, we identified the key physicochemical characteristics that significantly influence the distribution of endophytes, particularly in the case of OF. In contrast, CF was found to exert a more pronounced impact on the composition of the rhizosphere microbiome. Although the application of OF resulted in a broader spectrum of compounds in Huajuhong peel, CF proved to be more efficacious in elevating the concentrations of flavonoids and polysaccharides in the fruit.</p><p><strong>Discussion: </strong>Consequently, the effects of long-term application of OF or CF on medicinal plants is different in many ways. This research provides a guide for OF/CF selection from the perspective of soil microecology and aids us to critically assess and understand the effects of both fertilizers on the soil environment, and promotes sustainable development of organic agriculture.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575555","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}

{"title":"Comparative analysis of the leprosy detection rate regarding its clinical spectrum through PCR using the <i>16S rRNA</i> gene: a scientometrics and meta-analysis.","authors":"Marcos Jessé Abrahão Silva, Thiago Pinto Brasil, Caroliny Soares Silva, Cristiane Cunha Frota, Daniele Melo Sardinha, Luiza Raquel Tapajós Figueira, Keitty Anne Silva Neves, Everaldina Cordeiro Dos Santos, Karla Valéria Batista Lima, Nédia de Castilhos Ghisi, Luana Nepomuceno Gondim Costa Lima","doi":"10.3389/fmicb.2024.1497319","DOIUrl":"10.3389/fmicb.2024.1497319","url":null,"abstract":"<p><strong>Background: </strong>Leprosy is a chronic and disabling infectious disease caused by <i>Mycobacterium leprae</i>. It has a wide clinical spectrum and is operationally classified into paucibacillary (PB) and multibacillary (MB) cases. There is evidence that the <i>16S rRNA</i> gene can be used in Polymerase Chain Reaction (PCR) for complementary detection with high sensitivity and specificity. However, there is no literature convention on its diagnostic correspondence regarding the particular operational classification of the disease. This study aimed to correlate, through a meta-analysis, the detection rate of leprosy between the PCR method with the <i>16S rRNA</i> gene in the clinical forms PB and MB in relation to confirmed cases.</p><p><strong>Methods: </strong>This is a systematic review and meta-analysis study conducted according to the PRISMA 2020 guidelines, using the search descriptors with \"AND\": \"Leprosy\"; \"Polymerase Chain Reaction\"; \"<i>16S rRNA</i>\" in the PUBMED, SciELO, LILACS, and Science Direct databases. The search was limited to original observational articles in Portuguese, English, or Spanish, with no defined time frame. The methodological quality assessment of the selected articles was performed using the JBI checklists. A scientometric approach to the article using used the VOS Viewer and Scimago Graphica software. The meta-analysis was conducted using Comprehensive Meta-Analyses software, under Pearson's Correlation effect test and fixed effect model and subgroup analysis concerning the type of sample analyzed.</p><p><strong>Results: </strong>The study was significant from the perspective of the paucibacillary group (Clinical biopsy: -0.45 [95% CI= -0.63 - -0.22], <i>p</i> < 0.001/ Slit smear skin: -0.52 [95% CI= -0.65 - -0.36], <i>p</i> < 0.001 / Overall: -0.50 [95% CI= -0.61 - -0.37], <i>p</i> < 0.001). The PCR diagnostic method for the16S rRNAgene ofM. lepraehas low viability and diagnostic sensitivity in both clinical biopsy samples and leprosy skin smears.</p><p><strong>Conclusion: </strong>This implies little validation of it as a PCR target gene for diagnosing the disease, highlighting limitations in the actual technique.</p><p><strong>Systematic review registration: </strong>https://www.crd.york.ac.uk/prospero/, identifier CRD42024588790.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575583","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}

{"title":"A simple and cost-effective transformation system for <i>Porphyromonas gingivalis</i> via natural competence.","authors":"Kimihiro Abe, Hiroko Yahara, Ryoma Nakao, Takehiro Yamaguchi, Yukihiro Akeda","doi":"10.3389/fmicb.2024.1476171","DOIUrl":"10.3389/fmicb.2024.1476171","url":null,"abstract":"<p><p><i>Porphyromonas gingivalis</i> is a major oral bacterial pathogen responsible for severe periodontal diseases. Numerous studies have used genetic approaches to elucidate the molecular mechanisms underlying its pathogenicity. Typically, electroporation and conjugation are utilized for mutagenesis of <i>P. gingivalis</i>; however, these techniques require specialized equipment such as high-voltage electroporators, conjugative plasmids and donor strains. In this study, we present a simple, cost-effective transformation method for <i>P. gingivalis</i> without any special equipment by exploiting its natural DNA competence. <i>P. gingivalis</i> ATCC 33277 was grown to the early-exponential phase and mixed with a donor DNA cassette. This mixture was then spotted onto a BHI-HM blood-agar plate and incubated for one day to promote colony biofilm formation. The resulting colony biofilm was suspended in a liquid medium and spread onto antibiotic-containing agar plates. Transformants appeared within 4 to 5 days, achieving a maximum efficiency of 7.7 × 10⁶ CFU/μg. Although we optimized the transformation conditions using a representative strain ATCC 33277, but the method was also effective for other <i>P. gingivalis</i> strains, W83 and TDC60. Additionally, we discovered that deletion of <i>PGN_0421</i> or <i>PGN_0519</i>, encoding putative ComEA and ComEC, abolished competency, indicating that these gene products are essential for the natural competence.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575553","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}

{"title":"Fecal bile acid dysmetabolism and reduced ursodeoxycholic acid correlate with novel microbial signatures in feline chronic kidney disease.","authors":"John C Rowe, Stacie C Summers, Jessica M Quimby, Jenessa A Winston","doi":"10.3389/fmicb.2024.1458090","DOIUrl":"10.3389/fmicb.2024.1458090","url":null,"abstract":"<p><strong>Background: </strong>Microbial-derived secondary bile acids (SBAs) are reabsorbed and sensed via host receptors modulating cellular inflammation and fibrosis. Feline chronic kidney disease (CKD) occurs with progressive renal inflammation and fibrosis, mirroring the disease pathophysiology of human CKD patients.</p><p><strong>Methods: </strong>Prospective cross-sectional study compared healthy cats (<i>n</i> = 6) with CKD (IRIS Stage 2 <i>n</i> = 17, Stage 3 or 4 <i>n</i> = 11). Single timepoint fecal samples from all cats underwent targeted bile acid metabolomics. 16S rRNA gene amplicon sequencing using DADA2 with SILVA taxonomy characterized the fecal microbiota.</p><p><strong>Results: </strong>CKD cats had significantly reduced fecal concentrations (median 12.8 ng/mg, Mann-Whitney <i>p</i> = 0.0127) of the SBA ursodeoxycholic acid (UDCA) compared to healthy cats (median 39.4 ng/mg). Bile acid dysmetabolism characterized by <50% SBAs was present in 8/28 CKD and 0/6 healthy cats. Beta diversity significantly differed between cats with <50% SBAs and > 50% SBAs (PERMANOVA <i>p</i> < 0.0001). Twenty-six amplicon sequence variants (ASVs) with >97% nucleotide identity to <i>Peptacetobacter hiranonis</i> were identified. <i>P. hiranonis</i> combined relative abundance was significantly reduced (median 2.1%) in CKD cats with <50% SBAs compared to CKD cats with >50% SBAs (median 13.9%, adjusted <i>p</i> = 0.0002) and healthy cats with >50% SBAs (median 15.5%, adjusted <i>p</i> = 0.0112). <i>P. hiranonis</i> combined relative abundance was significantly positively correlated with the SBAs deoxycholic acid (Spearman <i>r</i> = 0.5218, adjusted <i>p</i> = 0.0407) and lithocholic acid (Spearman <i>r</i> = 0.5615, adjusted <i>p</i> = 0.0156). Three <i>Oscillospirales</i> ASVs and a <i>Roseburia</i> ASV were also identified as significantly correlated with fecal SBAs.</p><p><strong>Clinical and translational importance: </strong>The gut-kidney axis mediated through microbial-derived SBAs appears relevant to the spontaneous animal CKD model of domestic cats. This includes reduced fecal concentrations of the microbial-derived SBA UDCA, known to regulate inflammation and fibrosis and be reno-protective. Microbes correlated with fecal SBAs include <i>bai</i> operon containing <i>P. hiranonis</i>, as well as members of <i>Oscillospirales</i>, which also harbor a functional <i>bai</i> operon. Ultimately, CKD cats represent a translational opportunity to study the role of SBAs in the gut-kidney axis, including the potential to identify novel microbial-directed therapeutics to mitigate CKD pathogenesis in veterinary patients and humans alike.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575621","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}

{"title":"Lymphocystis viral disease impacts the diversity and functional profiles of the skin microbiome in gilthead seabream.","authors":"Raquel Xavier, Marcos Pérez-Losada, Sofia Marques Silva, Marilia Lino, Maria João Faleiro, Paula Canada","doi":"10.3389/fmicb.2024.1470572","DOIUrl":"10.3389/fmicb.2024.1470572","url":null,"abstract":"<p><p>Lymphocystis viral disease (LVD) is a highly transmissible disease known to affect multiple fishes worldwide. Although this disease is usually benign, mortalities can occur in cases where infection is severe or secondary infection with bacterial pathogens and parasites occur. However, little is known about the bacterial dynamics of fish with LVD or what bacterial pathogens may be responsible for secondary infections. Here we assessed the effects of LVD on the skin microbiome of gilthead seabream by comparing 30 symptomatic, asymptomatic and recovered (three weeks after infection) fish using 16S rRNA high-throughput sequencing. Our results show that LVD is associated with significant changes in microbiome structure and function. Importantly, fish pathogens like <i>Tenacibaculum maritimum</i> and some <i>Vibrio</i> species increased their abundance. Moreover, microbial metabolic activities of the commensal microbiota that may confer some protection to fish were suppressed in diseased fish. After reducing fish cage density to treat symptoms and three weeks of recovery, the abundance of pathogens was significantly reduced and microbiome functionality was recovered, although community structure remained significantly different. These results show that LVD can severely disrupt the bacterial communities of the skin of the gilthead seabream, leading to an increase in bacterial pathogens responsible for relevant diseases in gilthead seabream farms.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575626","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}

{"title":"<i>Helicobacter pylori</i> infection and inflammatory bowel disease: a 2-sample Mendelian randomization study.","authors":"Yurong Cui, Jinxin Li, Bing Zhao, Junying Liu","doi":"10.3389/fmicb.2024.1384285","DOIUrl":"10.3389/fmicb.2024.1384285","url":null,"abstract":"<p><strong>Introduction: </strong>Observational studies have discovered a contradictory phenomenon between <i>Helicobacter pylori (H. pylori)</i> infection and inflammatory bowel disease (IBD). The study aimed to confirm the causal association between <i>H. pylori</i> and IBD, including ulcerative colitis (UC) and Crohn's disease (CD).</p><p><strong>Methods: </strong>We conducted a Mendelian randomization (MR) study with two sample Genome-Wide Association Studies (GWAS) to determine whether there is a causal relationship between <i>H. pylori</i> infection and IBD, as well as the possible pathogenic factors that may be involved. The reliability of the main MR assumptions was examined through a series of sensitivity analyses.</p><p><strong>Results: </strong>Two genetic variants (SNPs) previously identified were employed as instrumental variables (IVs) for <i>H. pylori</i> infection. GWAS data for IBD, UC, and CD were obtained from the recent DF10 release10 of the FinnGen study. Our findings indicated a significant association between <i>H. pylori</i> seropositivity and an increased risk of IBD and UC (IBD: OR: 1.16, 95% CI, 1.03-1.31, <i>P</i> < 0.05; UC: OR: 1.22, 95% CI, 1.08-1.37, <i>P</i> < 0.001) while no causal relationship with CD (<i>P</i> > 0.05). Analysis of the main virulence pathogenic factors revealed a causal relationship between cytotoxin-associated protein A (CagA) and IBD and UC (IBD: OR: 1. 06, 95% CI, 1.001-1.11, <i>P</i> < 0.05; UC: OR: 1.07, 95% CI, 1.004-1.14, <i>P</i> < 0.05), while no correlation was found for vacuolar cytotoxin A (VacA) (<i>P</i> > 0.05). After applying the False Discovery Rate (FDR) correction, the causal relationship between CagA and the risk of IBD or UC was no longer statistically significant.</p><p><strong>Conclusion: </strong>This study suggests a potential causal relationship between H. pylori infection and IBD, particularly UC. The effect may be more pronounced in individuals with previous <i>H. pylori</i> infections.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575603","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}

{"title":"Endophytic bacteria in <i>Camellia reticulata</i> pedicels: isolation, screening and analysis of antagonistic activity against nectar yeasts.","authors":"Qingxin Meng, Rong Huang, Lijie Xun, Xiaoman Wu, Shangkao Deng, Dan Yue, Wenzheng Zhao, Xia Dong, Xueyang Gong, Kun Dong","doi":"10.3389/fmicb.2024.1459354","DOIUrl":"10.3389/fmicb.2024.1459354","url":null,"abstract":"<p><p><i>Camellia reticulata</i>, an ancient plant species endemic to Yunnan Province, China, remains underexplored in terms of its endophytic bacterial communities. The plant tissue pedicel serves as the connection between the flower and the stem, not only delivers nutrients but also transmits metabolic substances from endophytic bacteria to the nectar during long-term microbial colonization and probably improves the antagonistic activity of nectar against yeast. Hence, 138 isolates of endophytic bacteria have been isolated in this study from the pedicels of 12- and 60-year-old <i>C. reticulata</i>. Comparative analysis revealed significantly higher density of endophytic bacteria in older trees. Among these isolates, 29 exhibited inhibitory effects against nectar yeasts. Most of the isolates displayed positive results for Gram staining, catalase reaction, gelatin liquefaction, and motility. Additionally, the isolates demonstrated the ability to utilize diverse substrates, such as glucose, nitrate, and starch. Based on 16S rRNA molecular biology analysis, these isolates were identified to be 11 different species of 6 genera, with the majority belonging to <i>Bacillus</i> genus. Notably, C1 isolate, identified as <i>Bacillus spizizenii</i>, exhibited strongest antagonistic effect against three yeasts, i.e., <i>Metschnikowia reukaufii, Cryptococcus laurentii</i>, and <i>Rhodotorula glutinis</i>, with minimum inhibitory concentration values below 250 μg/mL. Major metabolites of <i>B. spizizenii</i> were aminoglycosides, beta-lactams, and quinolones, which possess antimicrobial activities. Furthermore, KEGG enrichment pathways primarily included the synthesis of plant secondary metabolites, phenylpropanoids, amino acids, alkaloids, flavonoids, neomycin, kanamycin, and gentamicin. Therefore, antagonistic activity of <i>B. spizizenii</i> against yeasts could be attributed to these antibiotics. The findings highlight the diverse endophytic bacteria associated with <i>C. reticulata</i>, indicating their potential as a valuable resource of bioactive metabolites. Additionally, this study provides new insights into the role of endophytic bacteria of pedicels in enhancing nectar resistance against yeasts.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575611","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}

{"title":"Structural and functional insights from the sequences and complex domain architecture of adhesin-like proteins from <i>Methanobrevibacter smithii</i> and <i>Methanosphaera stadtmanae</i>.","authors":"Anjali Bansal Gupta, Henning Seedorf","doi":"10.3389/fmicb.2024.1463715","DOIUrl":"10.3389/fmicb.2024.1463715","url":null,"abstract":"<p><p>Methanogenic archaea, or methanogens, are crucial in guts and rumens, consuming hydrogen, carbon dioxide, and other fermentation products. While their molecular interactions with other microorganisms are not fully understood, genomic sequences provide information. The first genome sequences of human gut methanogens, <i>Methanosphaera stadtmanae</i> and <i>Methanobrevibacter smithii</i>, revealed genes encoding adhesin-like proteins (ALPs). These proteins were also found in other gut and rumen methanogens, but their characteristics and functions remain largely unknown. This study analyzes the ALP repertoire of <i>M. stadtmanae</i> and <i>M. smithii</i> using AI-guided protein structure predictions of unique ALP domains. Both genomes encode more than 40 ALPs each, comprising over 10% of their genomes. ALPs contain repetitive sequences, many of which are unmatched in protein domain databases. We present unique sequence signatures of conserved ABD repeats in ALPs and propose a classification based on domain architecture. Our study offers insights into ALP features and how methanogens may interact with other microorganisms.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575629","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}

{"title":"Succeed to culture a novel lineage symbiotic bacterium of <i>Mollicutes</i> which widely found in arthropods intestine uncovers the potential double-edged sword ecological function.","authors":"Lingyu Zhang, Qi Chen, Shenzheng Zeng, Zhixuan Deng, Zhongcheng Liu, Xuanting Li, Qilu Hou, Renjun Zhou, Shicheng Bao, Dongwei Hou, Shaoping Weng, Jianguo He, Zhijian Huang","doi":"10.3389/fmicb.2024.1458382","DOIUrl":"10.3389/fmicb.2024.1458382","url":null,"abstract":"<p><p>Symbiotic gut bacteria play crucial role in host health. Symbionts are widely distributed in arthropod intestines, but their ecological functions are poorly understood due to the inability to cultivate them. Members of <i>Candidatus</i> Bacilliplasma (CB) are widely distributed in crustacean intestine and maybe commensals with hosts, but the paucity of pure cultures has limited further insights into their physiologies and functions. Here, four strains of representative CB bacteria in shrimp intestine were successfully isolated and identified as members of a novel Order in the Phylum <i>Mycoplasmatota</i>. Through genome assembly, the circular genome maps of the four strains were obtained, and the number of coding genes ranged from 1,886 to 1,980. Genomic analysis suggested that the bacteria were missing genes for many critical pathways including the TCA cycle and biosynthesis pathways for amino acids and coenzyme factors. The analysis of 16S amplification data showed that <i>Shewanella, Pseudomonas</i> and CB were the dominant at the genera level in the intestine of <i>Penaeus vannamei</i>. Ecological functional experiments revealed that the strains were symbionts and colonized shrimp intestines. Our valued findings can greatly enhance our understanding and provides new insights into the potentially significant role of uncultured symbiotic bacteria in modulating host health.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11527720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568394","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}

{"title":"Epidemiological dynamics and molecular characterization of HIV drug resistance in eastern China from 2020 to 2023.","authors":"Min Zhu, Zhou Sun, Xingliang Zhang, Wenjie Luo, Sisheng Wu, Ling Ye, Ke Xu, Junfang Chen","doi":"10.3389/fmicb.2024.1475548","DOIUrl":"10.3389/fmicb.2024.1475548","url":null,"abstract":"<p><strong>Objective: </strong>HIV drug resistance (HIVDR) has become a threat to the elimination of the AIDS epidemic due to the global scale-up of antiretroviral therapy (ART) for HIV-infected individuals. This study aims to investigate the epidemiological dynamics and molecular characterization of HIV pretreatment drug resistance (PDR) and acquired drug resistance (ADR) in Hangzhou, a developed region in China.</p><p><strong>Methods: </strong>An epidemiological survey combined with a molecular transmission network and Bayesian analysis was conducted. A total of 3,596 individuals with newly confirmed HIV infections (from 2020 to 2023) and 164 individuals with ART failure (from 2021 to 2023) were included. The molecular transmission network was used to identify key drug-resistant transmission clusters, while the Bayesian analysis was utilized to trace the origins and spread of these clusters.</p><p><strong>Results: </strong>The overall prevalence of PDR was found to be 8.4% (303/3596). Among these cases, PDR to non-nucleoside reverse transcriptase inhibitors (NNRTIs) accounted for 4.7% (170/3596), significantly higher than the resistance observed for protease inhibitors (PIs; 2.8%, <i>p</i> < 0.001) and nucleoside reverse transcriptase inhibitors (NRTIs; 1.4%, <i>p</i> < 0.001). Multivariate logistic regression analysis revealed a significantly higher PDR value among individuals infected with the CRF07_BC subtype compared to those with the CRF08_BC subtype (aOR = 0.56, 95% CI = 0.359-0.859, <i>p</i> = 0.008). The molecular transmission network analysis identified the transmission of the drug resistance mutation (DRM) Q58E within the clusters of the CRF07_BC subtype. The Bayesian analysis suggested that these clusters were introduced into Hangzhou from Shenzhen between 2005 and 2012. Furthermore, the study highlighted 50.6% (83/164) prevalence of ADR among individuals experiencing ART failure. The combined molecular network analysis of virological failure and newly confirmed HIV infections indicated the transmission of the K103N mutation between these groups.</p><p><strong>Conclusion: </strong>In conclusion, targeted interventions may be necessary for specific subtypes and transmission clusters to control the spread of drug-resistant HIV. Continuous monitoring of resistance patterns is critical to inform treatment strategies and optimize ART regimens.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11529039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568352","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}