Microbiology spectrum最新文献

{"title":"Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the <i>Embecovirus</i> subgenus.","authors":"Jordan D Zehr, Sergei L Kosakovsky Pond, Stephen D Shank, Holly McQueary, Jennifer K Grenier, Gary R Whittaker, Michael J Stanhope, Laura B Goodman","doi":"10.1128/spectrum.00867-24","DOIUrl":"10.1128/spectrum.00867-24","url":null,"abstract":"<p><p>There are several examples of coronaviruses in the Betacoronavirus subgenus <i>Embecovirus</i> that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as horses and donkeys, are susceptible to equine coronaviruses (ECoVs). With increased testing prevalence, several ECoV genome sequences have become available for molecular evolutionary analyses, especially those from the United States of America (USA). To date, no analyses have been performed to characterize evolution within coding regions of the ECoV genome. Here, we obtain and describe four new ECoV genome sequences from infected equines from across the USA presenting clinical symptoms of ECoV, and infer ECoV-specific and <i>Embecovirus</i>-wide patterns of molecular evolution. Within two of the four data sets analyzed, we find evidence of intra-host evolution within the nucleocapsid (N) gene, suggestive of quasispecies development. We also identify 12 putative genetic recombination events within the ECoV genome, 11 of which fall in ORF1ab. Finally, we infer and compare sites subject to positive selection on the ancestral branch of each major <i>Embecovirus</i> member clade. Specifically, for the two currently identified human coronavirus (HCoV) embecoviruses that have spilled from animals to humans (HCoV-OC43 and HCoV-HKU1), we find that there are 42 and 2 such sites, respectively, perhaps reflective of the more complex ancestral evolutionary history of HCoV-OC43, which involves several different animal hosts.IMPORTANCEThe Betacoronavirus subgenus <i>Embecovirus</i> contains coronaviruses that not only pose a health threat to animals and humans, but also have jumped from animal to human host. Equids, such as horses and donkeys are susceptible to equine coronavirus (ECoV) infections. No studies have systematically examined evolutionary patterns within ECoV genomes. Our study addresses this gap and provides insight into intra-host ECoV evolution from infected horses. Further, we identify and report natural selection pattern differences between two embecoviruses that have jumped from animals to humans [human coronavirus OC43 and HKU1 (HCoV-OC43 and HCoV-HKU1, respectively)], and hypothesize that the differences observed may be due to the different animal host(s) that each virus circulated in prior to its jump into humans. Finally, we contribute four novel, high-quality ECoV genomes to the scientific community.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0086724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381173","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":"Attenuated African swine fever viruses and the live vaccine candidates: a comprehensive review.","authors":"Jiaqi Fan, Haisheng Yu, Faming Miao, Junnan Ke, Rongliang Hu","doi":"10.1128/spectrum.03199-23","DOIUrl":"10.1128/spectrum.03199-23","url":null,"abstract":"<p><p>The African swine fever virus (ASFV) is spreading worldwide and causing huge economic losses to the global pig industry. The ASFV genome is 170-193 kb in length, contains approximately 150 open reading frames, and encodes more than 200 proteins, most of which have unknown functions. Owing to the unique viral structure, replication strategy, large number of genes of unknown function, and complicated pathogenesis, vaccine development research is challenging. Several naturally attenuated ASFV isolates have been extensively investigated and many genetically manipulated, gene-deleted, and cell-adapted ASFVs have been reported. Currently, live attenuated viruses prepared from weakly virulent strains are an efficient method to provide effective protection in vaccinated pigs; however, these have seldom been widely approved for vaccine use, except in Vietnam. Herein, we summarize the attenuated isolates or vaccine candidates for live vaccines derived from different sources, including naturally mutated, attenuated, cell-adapted, and genetically modified recombinant ASFVs. This will help to understand the gene function and immunogenicity of attenuated live ASFV, as well as the shortcomings of these viruses as vaccine candidates, and provide clues to prepare live, efficient, and safe vaccines for African swine fever.IMPORTANCEOutbreaks of African swine fever (ASF) have caused devastating losses to the global pig industry. Pigs immunized with ASFV attenuated virus can resist the lethal challenge of a strongly virulent virus. Here, we summarize the virulence of naturally mutated, cell-adapted, and genetically recombinant ASFV for pigs, and the protective effect after facing an attack challenge. We also analyze the advantages and disadvantages of ASFV attenuated viruses as vaccine candidates to provide clues for the preparation of efficient and safe live African swine fever vaccines.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0319923"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391824","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":"Characterizing the urobiome in geriatric males with chronic indwelling urinary catheters: an exploratory longitudinal study.","authors":"Emma Stewart, Baylie R Hochstedler-Kramer, Mark Khemmani, Nina M Clark, Jorge P Parada, Ahmer Farooq, Chirag Doshi, Alan J Wolfe, Fritzie S Albarillo","doi":"10.1128/spectrum.00941-24","DOIUrl":"10.1128/spectrum.00941-24","url":null,"abstract":"<p><p>The impact of chronic indwelling urinary catheters (IUCs) on the composition and stability of the urinary microbiota remains unknown. The primary aim of this study was to describe the urinary microbiomes of geriatric males with chronic IUCs. A secondary aim was to explore clinical catheter-associated urinary tract infection (CAUTI) courses of the participants. Geriatric male patients with chronic IUCs were followed longitudinally. Catheterized urine, catheter tips, and both urethral and periurethral swabs were collected from participants at monthly intervals. Microbes were isolated and identified from each specimen using an enhanced culture method called expanded quantitative urine culture (EQUC) and targeted 16S rRNA gene DNA sequencing. Microbial outcomes were examined both in the absence of urinary symptoms and in the context of clinical diagnosis of CAUTI. Ten male participants (mean age 86 years) were enrolled. Urinary microbiomes differed for each participant. However, within each individual, microbiomes were similar over time and across niches (bladder, catheter, urethra, and periurethra). Within-niche microbiomes differed across individuals, and this was observed over time. The most abundant bacteria isolated from all niches were known uropathogens. Six of 10 individuals met diagnostic criteria for CAUTI at least once during the 12-month observation period, but no evidence of this or antibiotic treatment/response was discernable in our monthly samples. The microbiomes of each participant were unique and remained similar over time and across niches. Longitudinal EQUC or 16S rRNA gene sequencing data could be useful to clinicians when diagnosing or treating possible CAUTI.IMPORTANCECatheter-associated urinary tract infections (CAUTIs) are serious but preventable nosocomial infections. The most common risk factor for developing CAUTI is prolonged use of indwelling urinary catheters (IUCs). This study provides the first longitudinal description of the urinary microbiomes of geriatric males with chronic IUCs, in the absence of urinary signs and symptoms, as a first step toward enhancing our knowledge of the impact of chronic IUCs on the composition and stability of the urinary microbiota. This is an understudied area, particularly for males.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0094124"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470029","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":"Acute stress and multicellular development alter the solubility of the <i>Dictyostelium</i> Sup35 ortholog ERF3.","authors":"Felicia N Williams, Kanesha L Travis, Holly N Haver, Anna D Umano, Yaneli Guerra-Hernandez, K Matthew Scaglione","doi":"10.1128/spectrum.01607-24","DOIUrl":"10.1128/spectrum.01607-24","url":null,"abstract":"<p><p>Among sequenced organisms, the genome of <i>Dictyostelium discoideum</i> is unique in that it encodes for a massive amount of repeat-rich sequences in the coding region of genes. This results in the <i>Dictyostelium</i> proteome encoding for thousands of repeat-rich proteins, with nearly 24% of the <i>Dictyostelium</i> proteome encoding Q/N-rich regions that are predicted to be prion like in nature. To begin investigating the role of prion-like proteins in <i>Dictyostelium</i>, we decided to investigate ERF3, the <i>Dictyostelium</i> ortholog of the well-characterized yeast prion protein Sup35. ERF3 lacks the Q/N-rich region required for prion formation in yeast, raising the question of whether this protein aggregates and has prion-like properties in <i>Dictyostelium</i>. Here, we found that ERF3 formed aggregates in response to acute cellular stress. However, unlike <i>bona fide</i> prions, we were unable to detect transmission of aggregates to progeny. We further found that aggregation of this protein is driven by the ordered C-terminal domain independently of the disordered N-terminal domain. Finally, we also observed aggregation of ERF3 under conditions that induce multicellular development, suggesting that this phenomenon may play a role in <i>Dictyostelium</i> development. Together, these findings suggest a role for regulated protein aggregation in <i>Dictyostelium</i> cells under stress and during development.IMPORTANCEPrion-like proteins have both beneficial and deleterious effects on cellular health, and many organisms have evolved distinct mechanisms to regulate the behaviors of these proteins. The social amoeba <i>Dictyostelium discoideum</i> contains the highest proportion of proteins predicted to be prion like and has mechanisms to suppress their aggregation. However, the potential roles and regulation of these proteins remain largely unknown. Here, we demonstrate that aggregation of the <i>Dictyostelium</i> translation termination factor ERF3 is induced by both acute cellular stress and by multicellular development. These findings imply that protein aggregation may have a regulated and functional role in the <i>Dictyostelium</i> stress response and during multicellular development.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0160724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350114","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":"Isolation of a <i>bla</i>_NDM-1-positive strain in Israel predating the earliest observations from India.","authors":"Frédéric Grenier, Vincent Baby, Sarah Allard, Simon Lévesque, François Papale, Richard Sullivan, Hannah L Landecker, Paul G Higgins, Sébastien Rodrigue, Louis-Patrick Haraoui","doi":"10.1128/spectrum.01002-24","DOIUrl":"10.1128/spectrum.01002-24","url":null,"abstract":"<p><p><i>bla</i>_NDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, is thought to have emerged in India, as its initial detection in 2008 was linked to this country, and subsequent retrospective surveys had so far established the earliest <i>bla</i>_NDM-positive strains to be isolated in India in 2005. Molecular dating and analyses suggest <i>bla</i>_NDM emerged within <i>Acinetobacter</i> species decades prior to 2005 on a Tn<i>125</i> transposon. Despite early reports of elevated rates of carbapenem-resistant <i>Acinetobacter</i> species in Israel starting in the 1990s, limited molecular data are available from this location. We searched for <i>bla</i>_NDM among <i>Acinetobacter</i> species isolated in Israel between 2001 and 2006. One <i>A. junii</i> strain, Ajun-H1-3, isolated in January 2004, carried <i>bla</i>_NDM-1 within a Tn<i>125</i>-like transposon on a 49-kb plasmid, pNDM-Ajun-H1-3, making Ajun-H1-3 the earliest NDM-positive isolate observed to date. The pNDM-Ajun-H1-3 plasmid matched numerous BJ01-like NDM-positive plasmids identified from 2005 onward in <i>Acinetobacter</i> species as well as Enterobacterales. These results indicate the need for further retrospective work on global strain archives to shed light on the conditions favoring the emergence as well as subsequent evolution and spread of <i>bla</i>_NDM.</p><p><strong>Importance: </strong>This study presents the earliest observation of <i>bla</i>_NDM-1, isolated in a geographical region distant from where it is believed to have originated. In doing so, this study provides novel insights into the emergence and spread of <i>bla</i>_NDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, and its associated mobile genetic elements. It also sheds light on the conditions that foster the evolution of antimicrobial resistance, one of the greatest public health challenges we face.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0100224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350137","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":"First report of IS<i>Kpn26</i> element mediating <i>mgrB</i> gene disruption in the ST1 colistin- and carbapenem-resistant <i>Klebsiella pneumoniae</i> cluster isolated from a patient with chest infection.","authors":"Xiaosi Li, Siquan Shen, Yan Feng, Heping Shen, Fupin Hu, Xiaoyan Wu","doi":"10.1128/spectrum.00952-24","DOIUrl":"10.1128/spectrum.00952-24","url":null,"abstract":"<p><p>Colistin is used as a last-line therapy against carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP). However, colistin resistance in <i>Klebsiella pneumoniae</i> is increasingly reported worldwide. This study aims to investigate the instrumental role of insertion sequence (IS) elements in colistin resistance through <i>mgrB</i> disruption in <i>K. pneumoniae</i> during treatment. Five clinical isolates of CRKP, designated KPN1~KPN5 were collected from the lower respiratory tract of a patient with chest infection before and after treatment with colistin. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole genome sequencing and bioinformatics were used to analyze the sequence types (STs), resistance genes, and genetic characteristics of the five isolates of <i>K. pneumoniae</i>. Antimicrobial susceptibility testing indicated that all five <i>K. pneumoniae</i> isolates were resistant to cephalosporins (ceftriaxone, ceftazidime, and cefepime), several carbapenems (imipenem, meropenem), cefoperazone-sulbactam, piperacillin-tazobactam, ciprofloxacin, and fosfomycin, whereas they were sensitive to amikacin and tigecycline. In addition, three of these isolates were resistant to colistin, with minimum inhibitory concentration values of >8 mg/L. Whole genome sequencing revealed that all five <i>K. pneumoniae</i> isolates belonged to sequence type 1 (ST1), which shared an identical <i>bla</i>_KPC-2. Notably, disruption of <i>mgrB</i> by the IS<i>Kpn26</i> insertion sequence was shown to be the primary colistin resistance mechanism during the treatment. To our knowledge, this is the first report of IS<i>Kpn26</i> element mediating <i>mgrB</i> disruption in the ST1 colistin and CRKP obtained from a patient with chest infection in mainland China. This study provides new research ideas to explore the clinical drug resistance mechanism of CRKP and the critical need to monitor and understand resistance mechanisms to preserve the efficacy of last-line antibiotics such as colistin.</p><p><strong>Importance: </strong>Of note, this chapter gives an update on colistin resistance in sequence type 1 <i>Klebsiella pneumoniae</i>, by focusing on the <i>mgrB</i> disrupted by IS<i>Kpn26</i> element.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0095224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308144","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":"Validation of the Diabetomics CovAB SARS-CoV-2 antibody test in children: comparison with serology.","authors":"Manisha Gurumurthy, Joseph Schwab, Sri Ram Pentakota, Rahul Ukey, Maria Gennaro, Pauline Thomas, Stephen Friedman","doi":"10.1128/spectrum.00646-24","DOIUrl":"10.1128/spectrum.00646-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Monitoring antibody prevalence is a valuable tool to evaluate the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a community, identify risk factors, and assess the impact of clinical and public health intervention strategies. The antibody prevalence of SARS-CoV-2 in children in the United States in early 2022 was estimated by the Centers for Disease Control and Prevention to be 74.2%, using seroprevalence from a variety of sources. A study by the New Jersey Department of Health in late 2022/early 2023 in unvaccinated children found a lower prevalence, 68% when using a gum swab method to detect antibodies. This study compared the accuracy of the gum swab method to detect antibodies with simultaneously obtained serological samples in additional children. This cross-sectional study recruited well children, not vaccinated for SARS-CoV-2, aged 18 months to 11 years, who were scheduled for routine bloodwork at an inner-city university-based pediatric clinic. With parental consent, an extra 5 cc of blood and a gum swab sample were collected. Results from Diabetomics CovAb SARS-CoV-2 gum swab antibody test and Rutgers New Jersey Medical School enzyme-linked immunosorbent assay serology test for spike protein antibody were compared. The seropositivity of these paired samples was compared using McNemar's test, Cohen's kappa statistic, and other diagnostic accuracy statistics. From June through August 2023, 86 children were recruited. Antibody positivity by gum swab was 70.9% and by serology was 87.2%. The Cohen's kappa statistic was 0.39 indicating minimal agreement and McNemar's test was significant (&lt;i&gt;P&lt;/i&gt;-value of 0.0010). Compared with serology, gum swab was 78.7% sensitive (95% CI 68.7% to 87.3%) and 81.8% specific (95% CI 48.2% to 97.7%). Positive and negative predictive values were 97.5% and 29.9%, respectively, and accuracy was 79.0%. Sensitivity in non-Hispanic versus Hispanic children was 74.2% versus 82.5%, and in children 6-11 years versus 18 months to 5 years, it was 74.2% versus 81.8%. While the gum swab method of antibody detection is not as sensitive or specific as serology, sample collection can be done in settings where phlebotomy is not feasible. This method could be useful in non-clinical settings such as surveillance, for assessing epidemiological trends and associations.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Recently a study determining the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in unvaccinated children in NJ (Katic et al. 2023. Pediatric Academic Societies Meeting; Washington, D.C. https://2023.pas-meeting.org/searchbyposterbucket.asp?bm=Public+Health+%26+Prevention&t=Public+Health+%26+Prevention&pfp=Track) was conducted using a gum swab method for antibody detection. The Diabetomics CovAB test, which qualitatively identifies antibodies to SARS-CoV-2 spike protein, is a point-of-care, low-cost test, that is easy to administer in children. While this test p","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0064624"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470108","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":"Uncovering new <i>Firmicutes</i> species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.","authors":"Douglas Terra Machado, Beatriz do Carmo Dias, Rodrigo Cayô, Ana Cristina Gales, Fabíola Marques de Carvalho, Ana Tereza Ribeiro Vasconcelos","doi":"10.1128/spectrum.02113-24","DOIUrl":"10.1128/spectrum.02113-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the &lt;i&gt;Firmicutes&lt;/i&gt; phylum. We identified potential new species in the classes &lt;i&gt;Clostridia&lt;/i&gt; (&lt;i&gt;Borkfalkiaceae&lt;/i&gt;, &lt;i&gt;Lachnospiraceae&lt;/i&gt;, &lt;i&gt;Monoglobaceae&lt;/i&gt;, and &lt;i&gt;Oscillospiraceae&lt;/i&gt; families) and &lt;i&gt;Bacilli&lt;/i&gt; (&lt;i&gt;Bacillaceae&lt;/i&gt; and &lt;i&gt;Erysipelotrichaceae&lt;/i&gt; families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that &lt;i&gt;Clostridia&lt;/i&gt; and &lt;i&gt;Bacilli&lt;/i&gt; have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within &lt;i&gt;Clostridia&lt;/i&gt;, &lt;i&gt;Bacilli&lt;/i&gt;, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel &lt;i&gt;Firmicutes&lt;/i&gt; species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to &lt;i&gt;Clostridia&lt;/i&gt;, &lt;i&gt;Bacilli&lt;/i&gt;, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for micro","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0211324"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291321","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 conserved two-component system senses intracellular iron levels and regulates redox balance in <i>Mycobacterium</i> spp.","authors":"Rahul Yadav, Deepak Kumar Saini","doi":"10.1128/spectrum.01106-24","DOIUrl":"10.1128/spectrum.01106-24","url":null,"abstract":"<p><p>For bacteria, an intricate coordination between sensing and regulating iron levels and managing oxidative stress is required as their levels are tightly interlinked. While various oxidative stress and heme-based redox sensors have been reported for both pathogenic and non-pathogenic bacteria, the mechanisms governing the modulation of intracellular iron levels in response to changes in redox status remain unclear. In this study, a gene-inactivated strain of mycobacterial sensor kinase PdtaS showed dysregulated expression of genes associated with iron metabolism, including Fe-S clusters, NADH dehydrogenases, and iron uptake. The strain showed poor growth in nutrient-limiting conditions, a defect rescuable by heme but not by Fe³⁺ supplementation. This observation was associated with the PAS domain of the PdtaS sensor kinase. Biochemical and biophysical experiments established heme-binding to the PAS domain and its inhibitory effect on PdtaS auto-kinase activity, suggesting that the absence of heme induces activation of this sensor kinase. Interestingly, despite having an endogenous heme biosynthetic pathway or even external heme supplementation, the ∆<i>pdtaS</i> mutant exhibited persistent low intracellular iron levels concomitant with elevated oxidative stress. Antioxidant supplementation mitigated growth defects, emphasizing the link between oxidative stress, intracellular iron levels, and PdtaS activity. RNA-IP identified key targets associated with redox homeostasis and iron metabolism as targets of the PdtaR response regulator. The study proposes a novel role for the PdtaS-PdtaR TCS in sensing heme, regulation of intracellular iron levels, and redox balance.IMPORTANCEThe research article investigates the intricate interplay between bacteria's ability to take and utilize iron without inducing excess iron's toxic effects, including oxidative stress. The study shows that bacteria achieve this by sensing intracellular iron available as heme through a sensory protein PdtaS, which turns off when heme is in excess and prevents iron uptake and iron efflux. The process shields bacteria from generating Fe-dependent free radicals and allows it to maintain viability. The absence of sensor kinase abrogates all these processes, increasing bacteria susceptibility to ROS and thereby slowing growth. This feature of the sensor kinase PdtaS makes it an attractive co-therapeutic target for tuberculosis therapy, where its inhibition will prevent iron uptake, even in the presence of low iron, thereby halting bacterial proliferation.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0110624"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308138","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":"Seasonal succession of endophyte and the association with active ingredients in <i>Rheum palmatum</i>.","authors":"Ni Li, YiFan Mao, YaLi Huang, LingXuan Zhang, Lu Hou, XiaoJun Liu, YaRong Du, DaWei Chen, Kun Sun","doi":"10.1128/spectrum.01184-24","DOIUrl":"10.1128/spectrum.01184-24","url":null,"abstract":"<p><p>The endophyte is closely related to medicinal plant growth and development, stress resistance, and active ingredients' accumulation. However, a seasonal succession of endophytes and the association with active ingredients is still unclear. In this study, we used high-throughput sequencing methods to compare the endophyte diversity of <i>Rheum palmatum</i> under different seasons and analyze the association between endophytes and five active ingredients. The results show that the diversity of endophytic fungi increased and then decreased, while bacterial diversity increased with the change of season. Community composition showed that the dominant genera of endophytic fungi were different under the different seasons, while the dominant genera of endophytic bacteria were <i>Delftia</i>. Analysis of co-occurrence network maps showed that the connectivity and complexity of endophytic fungi and bacterial networks decreased with the change of season. Spearman analysis indicated that the active ingredients of <i>R. palmatum</i> were significantly positive correlation with genera of endophytic fungi (<i>Chalara</i>). FUNGuild and PICRUSt predictive analysis indicated that the function of endophytic fungi and bacteria, respectively, were symbiotroph and metabolism, and relative abundances were different under the different seasons. Our results help elucidate the mechanism of medicinal plant-endophyte interaction.</p><p><strong>Importance: </strong>Through the investigation of the seasonal succession of endophytes and the association with active ingredients in <i>Rheum palmatum</i>, we found that the diversity and composition of endophytes in <i>R. palmatum</i> exhibited seasonal dynamics, and the active ingredients of <i>R. palmatum</i> showed a significantly positive correlation with the genus of endophytic fungi (<i>Chalara</i>). Our results may lay a foundation for understanding the interaction mechanism of endophyte and medicinal plant, and can also provide a theoretical basis for sustainable production of medicinal plants.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0118424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308150","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}