ISME communications最新文献

{"title":"pH selects for distinct N₂O-reducing microbiomes in tropical soil microcosms.","authors":"Yanchen Sun, Yongchao Yin, Guang He, Gyuhyon Cha, Héctor L Ayala-Del-Río, Grizelle González, Konstantinos T Konstantinidis, Frank E Löffler","doi":"10.1093/ismeco/ycae070","DOIUrl":"10.1093/ismeco/ycae070","url":null,"abstract":"<p><p>Nitrous oxide (N₂O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N₂O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N₂O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N₂O assessed N₂O reduction at pH 4.5 and 7.3. All microcosms consumed N₂O, with lag times of up to 7 months observed in microcosms with 2 mM N₂O. Comparative metagenome analysis revealed that <i>Rhodocyclaceae</i> dominated in circumneutral microcosms under both N₂O feeding regimes. At pH 4.5, <i>Peptococcaceae</i> dominated in high-N₂O, and <i>Hyphomicrobiaceae</i> in low-N₂O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N₂O-reducing microcosms harbored <i>nos</i> operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type <i>nosZ</i> and lacking nitrite reductase genes (<i>nirS</i>/<i>K</i>). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N₂O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that <i>nosZ</i> genes commonly occur, suggesting broad distribution of N₂O reduction potential in acidic soils.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae070"},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11131594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.","authors":"Tong Wang, Leyuan Li, Daniel Figeys, Yang-Yu Liu","doi":"10.1093/ismeco/ycae063","DOIUrl":"10.1093/ismeco/ycae063","url":null,"abstract":"<p><p>The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed <i>in vitro</i> cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins' metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae063"},"PeriodicalIF":5.1,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11131966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining compositional data sets introduces error in covariance network reconstruction.","authors":"James D Brunner, Aaron J Robinson, Patrick S G Chain","doi":"10.1093/ismeco/ycae057","DOIUrl":"10.1093/ismeco/ycae057","url":null,"abstract":"<p><p>Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae057"},"PeriodicalIF":0.0,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11135214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into <i>Candidatus</i> Accumulibacter.","authors":"Xiaojing Xie, Xuhan Deng, Jinling Chen, Liping Chen, Jing Yuan, Hang Chen, Chaohai Wei, Xianghui Liu, Guanglei Qiu","doi":"10.1093/ismeco/ycae049","DOIUrl":"10.1093/ismeco/ycae049","url":null,"abstract":"<p><p><i>Candidatus</i> Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality <i>Ca</i>. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the <i>Ca</i>. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that <i>Ca</i>. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying <i>Ca</i>. Accumulibacter. A pan-genomic analysis with other <i>Ca</i>. Accumulibacter members suggested that all <i>Ca</i>. Accumulibacter likely has the potential to use dicarboxylic amino acids. <i>Ca</i>. Accumulibacter aalborgensis AALB and <i>Ca</i>. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for <i>Ca</i>. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of <i>Ca</i>. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae049"},"PeriodicalIF":5.1,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11131965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The endosymbiont of <i>Epithemia clementina</i> is specialized for nitrogen fixation within a photosynthetic eukaryote.","authors":"Solène L Y Moulin, Sarah Frail, Thomas Braukmann, Jon Doenier, Melissa Steele-Ogus, Jane C Marks, Matthew M Mills, Ellen Yeh","doi":"10.1093/ismeco/ycae055","DOIUrl":"10.1093/ismeco/ycae055","url":null,"abstract":"<p><p><i>Epithemia</i> spp. diatoms contain obligate, nitrogen-fixing endosymbionts, or diazoplasts, derived from cyanobacteria. These algae are a rare example of photosynthetic eukaryotes that have successfully coupled oxygenic photosynthesis with oxygen-sensitive nitrogenase activity. Here, we report a newly-isolated species, <i>E. clementina</i>, as a model to investigate endosymbiotic acquisition of nitrogen fixation. We demonstrate that the diazoplast, which has lost photosynthesis, provides fixed nitrogen to the diatom host in exchange for fixed carbon. To identify the metabolic changes associated with this endosymbiotic specialization, we compared the <i>Epithemia</i> diazoplast with its close, free-living cyanobacterial relative, <i>Crocosphaera subtropica</i>. Unlike <i>C. subtropica</i>, in which nitrogenase activity is temporally separated from photosynthesis, we show that nitrogenase activity in the diazoplast is continuous through the day (concurrent with host photosynthesis) and night. Host and diazoplast metabolism are tightly coupled to support nitrogenase activity: Inhibition of photosynthesis abolishes daytime nitrogenase activity, while nighttime nitrogenase activity no longer requires cyanobacterial glycogen storage pathways. Instead, import of host-derived carbohydrates supports nitrogenase activity throughout the day-night cycle. Carbohydrate metabolism is streamlined in the diazoplast compared to <i>C. subtropica</i> with retention of the oxidative pentose phosphate pathway and oxidative phosphorylation. Similar to heterocysts, these pathways may be optimized to support nitrogenase activity, providing reducing equivalents and ATP and consuming oxygen. Our results demonstrate that the diazoplast is specialized for endosymbiotic nitrogen fixation. Altogether, we establish a new model for studying endosymbiosis, perform a functional characterization of this diazotroph endosymbiosis, and identify metabolic adaptations for endosymbiotic acquisition of a critical biological function.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae055"},"PeriodicalIF":0.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.","authors":"Víctor Hugo Jarquín-Díaz, Susana Carolina Martins Ferreira, Alice Balard, Ľudovít Ďureje, Milos Macholán, Jaroslav Piálek, Johan Bengtsson-Palme, Stephanie Kramer-Schadt, Sofia Kirke Forslund-Startceva, Emanuel Heitlinger","doi":"10.1093/ismeco/ycae053","DOIUrl":"10.1093/ismeco/ycae053","url":null,"abstract":"<p><p>Antibiotic resistance is a priority public health problem resulting from eco-evolutionary dynamics within microbial communities and their interaction at a mammalian host interface or geographical scale. The links between mammalian host genetics, bacterial gut community, and antimicrobial resistance gene (ARG) content must be better understood in natural populations inhabiting heterogeneous environments. Hybridization, the interbreeding of genetically divergent populations, influences different components of the gut microbial communities. However, its impact on bacterial traits such as antibiotic resistance is unknown. Here, we present that hybridization might shape bacterial communities and ARG occurrence. We used amplicon sequencing to study the gut microbiome and to predict ARG composition in natural populations of house mice (<i>Mus musculus</i>). We compared gastrointestinal bacterial and ARG diversity, composition, and abundance across a gradient of pure and hybrid genotypes in the European House Mouse Hybrid Zone. We observed an increased overall predicted richness of ARG in hybrid mice. We found bacteria-ARG interactions by their co-abundance and detected phenotypes of extreme abundances in hybrid mice at the level of specific bacterial taxa and ARGs, mainly multidrug resistance genes. Our work suggests that mammalian host genetic variation impacts the gut microbiome and chromosomal ARGs. However, it raises further questions on how the mammalian host genetics impact ARGs via microbiome dynamics or environmental covariates.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae053"},"PeriodicalIF":0.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chlamydiae in corals: shared functional potential despite broad taxonomic diversity.","authors":"Justin Maire, Astrid Collingro, Matthias Horn, Madeleine J H van Oppen","doi":"10.1093/ismeco/ycae054","DOIUrl":"10.1093/ismeco/ycae054","url":null,"abstract":"<p><p>Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae054"},"PeriodicalIF":5.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140853788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures.","authors":"Haidi Xu, Nicholas A Pudlo, Thaisa M Cantu-Jungles, Yunus E Tuncil, Xin Nie, Amandeep Kaur, Bradley L Reuhs, Eric C Martens, Bruce R Hamaker","doi":"10.1093/ismeco/ycae037","DOIUrl":"https://doi.org/10.1093/ismeco/ycae037","url":null,"abstract":"<p><p>Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight <i>Bacteroides</i> xylan-degrading strains. For example, <i>Bacteroides cellulosilyticus</i> DSM 14838 (<i>Bacteroides cellulosilyticus</i>) grew well on an array of complex and simple structures, while <i>Bacteroides ovatus</i> 3-1-23 grew well only on the simple structures. In a competition experiment, <i>B. cellulosilyticus</i> growth was favored over <i>B. ovatus</i> on the complex AX-based structure. On the other hand, on the simple structure, <i>B. ovatus</i> strongly outcompeted <i>B. cellulosilyticus</i>, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae037"},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11032216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants.","authors":"Zhe Pan, Tao Ma, Michael Steele, Le Luo Guan","doi":"10.1093/ismeco/ycae044","DOIUrl":"https://doi.org/10.1093/ismeco/ycae044","url":null,"abstract":"<p><p>Perturbations and modulations during early life are vital to affect gut microbiome assembly and establishment. In this study, we assessed how microbial communities shifted during calf diarrhea and with probiotic yeast supplementation (<i>Saccharomyces cerevisiae var. boulardii</i>, SCB) and determined the key bacterial taxa contributing to the microbial assembly shifts using a total of 393 fecal samples collected from 84 preweaned calves during an 8-week trial. Our results revealed that the microbial assembly patterns differed between healthy and diarrheic calves at 6- and 8-week of the trial, with healthy calves being stochastic-driven and diarrheic calves being deterministic-driven. The two-state Markov model revealed that SCB supplementation had a higher possibility to shift microbial assembly from deterministic- to stochastic-driven in diarrheic calves. Furthermore, a total of 23 and 21 genera were specific ecotypes to assembly patterns in SCB-responsive (SCB-fed calves did not exhibit diarrhea) and nonresponsive (SCB-fed calves occurred diarrhea) calves, respectively. Among these ecotypes, the area under a receiver operating characteristic curve revealed that <i>Blautia</i> and <i>Ruminococcaceae</i> UCG 014, two unidentified genera from the <i>Ruminococcaceae</i> family, had the highest predictiveness for microbial assembly patterns in SCB-responsive calves, while <i>Prevotellaceae</i>, <i>Blautia</i>, and <i>Escherichia-Shigella</i> were the most predictive bacterial taxa for microbial assembly patterns in SCB-nonresponsive calves. Our study suggests that microbiome perturbations and probiotic yeast supplementation serving as deterministic factors influenced assembly patterns during early life with critical genera being predictive for assembly patterns, which sheds light on mechanisms of microbial community establishment in the gut of neonatal calves during early life.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae044"},"PeriodicalIF":0.0,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11033733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-occurring microflora and mucin drive <i>Pseudomonas aeruginosa</i> diversification and pathoadaptation.","authors":"Michael J Bottery, Helle Krogh Johansen, Jon W Pitchford, Ville-Petri Friman","doi":"10.1093/ismeco/ycae043","DOIUrl":"https://doi.org/10.1093/ismeco/ycae043","url":null,"abstract":"<p><p>While several environmental factors contribute to the evolutionary diversification of the pathogenic bacterium <i>Pseudomonas aeruginosa</i> during cystic fibrosis lung infections, relatively little is known about the impact of the surrounding microbiota. By using <i>in vitro</i> experimental evolution<i>,</i> we show that the presence of <i>Stenotrophomonas maltophilia</i>, <i>Staphylococcus aureus,</i> or them both, prevent the evolution of loss of virulence, which repeatedly occurs in the absence of these species due to mutations in regulators of the <i>Pseudomonas</i> Quinolone Signal quorum sensing system, <i>vqsM</i> and <i>pqsR</i>. Moreover, the strength of the effect of co-occurring species is attenuated through changes in the physical environment by the addition of mucin, resulting in selection for phenotypes resembling those evolved in the absence of the co-occurring species. Together, our findings show that variation in mucosal environment and the surrounding polymicrobial environment can determine the evolutionary trajectory of <i>P. aeruginosa</i>, partly explaining its diversification and pathoadaptation from acute to chronic phenotype during cystic fibrosis lung infections.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae043"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140873732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}