scholarly journals Evolution of Secondary Metabolite Genes in Three Closely Related Marine Actinomycete Species

2011 ◽  
Vol 77 (20) ◽  
pp. 7261-7270 ◽  
Author(s):  
Kelle C. Freel ◽  
Sang-Jip Nam ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
Secondary Metabolites ◽  
Bacterial Species ◽  
Closely Related Species ◽  
Vertical Inheritance ◽  
Content Type ◽  
Complex Processes ◽  
Marine Actinomycete ◽  
Species Specific ◽  
First Time ◽  
Related Compounds

ABSTRACTThe marine actinomycete genusSalinisporais composed of three closely related species. These bacteria are a rich source of secondary metabolites, which are produced in species-specific patterns. This study examines the distribution and phylogenetic relationships of genes involved in the biosynthesis of secondary metabolites in the salinosporamide and staurosporine classes, which have been reported forS. tropicaandS. arenicola, respectively. The focus is on “Salinispora pacifica,” the most recently discovered and phylogenetically diverse member of the genus. Of 61S. pacificastrains examined, 15 tested positive for a ketosynthase (KS) domain linked to the biosynthesis of salinosporamide K, a new compound in the salinosporamide series. Compound production was confirmed in two strains, and the domain phylogeny supports vertical inheritance from a common ancestor shared withS. tropica, which produces related compounds in the salinosporamide series. There was no evidence for interspecies recombination amongsalAKS sequences, providing further support for the geographic isolation of these two salinosporamide-producing lineages. In addition, staurosporine production is reported for the first time forS. pacifica, with 24 of 61 strains testing positive forstaD, a key gene involved in the biosynthesis of this compound. High levels of recombination were observed betweenstaDalleles inS. pacificaand the cooccurring yet more distantly relatedS. arenicola, which produces a similar series of staurosporines. The distributions and phylogenies of the biosynthetic genes examined provide insight into the complex processes driving the evolution of secondary metabolism among closely related bacterial species.

scholarly journals Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for FiveBacillusSpecies Relevant for Use as Animal Feed Additives or for Plant Protection

2018 ◽  
Vol 84 (19) ◽  
Author(s):  
Yvonne Agersø ◽  
Birgitte Stuer-Lauridsen ◽  
Karin Bjerre ◽  
Michelle Geervliet Jensen ◽  
Eric Johansen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Animal Feed ◽  
Bacterial Species ◽  
Feed Additives ◽  
Content Type ◽  
Cutoff Values ◽  
Antimicrobial Resistance Genes ◽  
Species Specific

ABSTRACTBacillus megaterium(n= 29),Bacillus velezensis(n= 26),Bacillus amyloliquefaciens(n= 6),Bacillus paralicheniformis(n= 28), andBacillus licheniformis(n= 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C forB. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in oneB. megateriumstrain with an elevated chloramphenicol MIC compared to the otherB. megateriumstrains. InB. velezensisandB. amyloliquefaciens, a putative tetracycline efflux gene,tet(L), was found in all strains (n= 27) with reduced tetracycline susceptibility but was absent in susceptible strains. AllB. paralicheniformisand 23% ofB. licheniformisstrains had elevated MICs for erythromycin and harboredermD. The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCEWhen commercializing bacterial strains, likeBacillusspp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for fiveBacillusspecies were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.

scholarly journals Lower Airway Bacterial Colonization Patterns and Species-Specific Interactions in Chronic Obstructive Pulmonary Disease

2018 ◽  
Vol 56 (10) ◽  
Author(s):  
David M. Jacobs ◽  
Heather M. Ochs-Balcom ◽  
Jiwei Zhao ◽  
Timothy F. Murphy ◽  
Sanjay Sethi
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Pulmonary Disease ◽  
Bacterial Colonization ◽  
Bacterial Species ◽  
Chronic Obstructive ◽  
Specific Interactions ◽  
Obstructive Pulmonary Disease ◽  
Content Type ◽  
Copd Patients ◽  
Species Specific

ABSTRACT Little is known about interactions between nontypeable Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, and Pseudomonas aeruginosa in the lower respiratory tract in chronic obstructive pulmonary disease (COPD) patients. We characterized colonization by these four bacterial species, determined species-specific interactions, and estimated the effects of host factors on bacterial colonization among COPD patients. We conducted a prospective cohort study in veterans with COPD that involved monthly clinical assessment and sputum cultures with an average duration of follow-up of 4.5 years. Cultures were used for bacterial identification. We analyzed bacterial interactions using generalized linear mixed models after controlling for clinical and demographic variables. The outcomes of interest were the relationships between bacteria based on clinical status (stable or exacerbation). One hundred eighty-one participants completed a total of 8,843 clinic visits, 30.8% of which had at least one of the four bacteria isolated. H. influenzae was the most common bacterium isolated (14.4%), followed by P. aeruginosa (8.1%). In adjusted models, S. pneumoniae colonization was positively associated with H. influenzae colonization (odds ratio [OR], 2.79; 95% confidence interval [CI], 2.03 to 3.73). We identified negative associations between P. aeruginosa and H. influenzae (OR, 0.15; 95% CI, 0.10 to 0.22) and P. aeruginosa and M. catarrhalis (OR, 0.51; 95% CI, 0.35 to 0.75). Associations were similar during stable and exacerbation visits. Recent antimicrobial therapy was associated with a lower prevalence of S. pneumoniae, H. influenzae, and M. catarrhalis, but not P. aeruginosa. Our findings support the presence of specific interspecies interactions between common bacteria in the lower respiratory tracts of COPD patients. Further work is necessary to elucidate the mechanisms of these complex interactions that shift bacterial species.

scholarly journals EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

2022 ◽  
Author(s):  
Mark Achtman ◽  
Zhemin Zhou ◽  
Jane Charlesworth ◽  
Laura A. Baxter
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Automated Identification ◽  
Bacterial Genomes ◽  
Bacterial Populations ◽  
Vertical Inheritance ◽  
Definition Of ◽  
Taxonomic Assignments ◽  
Species Specific ◽  
Sequence Types

The definition of bacterial species is traditionally a taxonomic issue while defining bacterial populations is done with population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST alleles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate the ability of HierCC to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and revealed differences in vertical inheritance of O serogroups. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.

scholarly journals Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Laura M. Carroll ◽  
Martin Wiedmann ◽  
Jasna Kovac
Keyword(s):  
Bacillus Cereus ◽  
Bacterial Species ◽  
Foodborne Pathogen ◽  
Bacterial Taxonomy ◽  
Closely Related Species ◽  
Important Species ◽  
Content Type ◽  
Bioterrorism Agent ◽  
Current Species ◽  
Species Definitions

ABSTRACT The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis. Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of ≈92.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at ≈92.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness. IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.

scholarly journals Lysobacter enzymogenes Uses Two Distinct Cell-Cell Signaling Systems for Differential Regulation of Secondary-Metabolite Biosynthesis and Colony Morphology

2013 ◽  
Vol 79 (21) ◽  
pp. 6604-6616 ◽  
Author(s):  
Guoliang Qian ◽  
Yulan Wang ◽  
Yiru Liu ◽  
Feifei Xu ◽  
Ya-Wen He ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Cell Signaling ◽  
Secondary Metabolite ◽  
Colony Morphology ◽  
Content Type ◽  
Signaling Systems ◽  
Lysobacter Enzymogenes ◽  
Bioactive Secondary Metabolites ◽  
Secondary Metabolite Biosynthesis ◽  
First Time

ABSTRACTLysobacter enzymogenesis a ubiquitous environmental bacterium that is emerging as a potentially novel biological control agent and a new source of bioactive secondary metabolites, such as the heat-stable antifungal factor (HSAF) and photoprotective polyene pigments. Thus far, the regulatory mechanism(s) for biosynthesis of these bioactive secondary metabolites remains largely unknown inL. enzymogenes. In the present study, the diffusible signal factor (DSF) and diffusible factor (DF)-mediated cell-cell signaling systems were identified for the first time fromL. enzymogenes. The results show that both Rpf/DSF and DF signaling systems played critical roles in modulating HSAF biosynthesis inL. enzymogenes. Rpf/DSF signaling and DF signaling played negative and positive effects in polyene pigment production, respectively, with DF playing a more important role in regulating this phenotype. Interestingly, only Rpf/DSF, but not the DF signaling system, regulated colony morphology ofL. enzymgenes. Both Rpf/DSF and DF signaling systems were involved in the modulation of expression of genes with diverse functions inL. enzymogenes, and their own regulons exhibited only a few loci that were regulated by both systems. These findings unveil for the first time new roles of the Rpf/DSF and DF signaling systems in secondary metabolite biosynthesis ofL. enzymogenes.

scholarly journals Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

2016 ◽  
Vol 198 (20) ◽  
pp. 2829-2840 ◽  
Author(s):  
Alejandra Culebro ◽  
Joana Revez ◽  
Ben Pascoe ◽  
Yasmin Friedmann ◽  
Matthew D. Hitchings ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Dynamics ◽  
Chemical Composition ◽  
Phenotypic Diversity ◽  
Host Adaptation ◽  
Campylobacter Coli ◽  
Genomic Information ◽  
Content Type ◽  
Species Specific ◽  
First Time

ABSTRACTDespite the importance of lipooligosaccharides (LOSs) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS inCampylobacter coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelatedC. coliisolates sampled from several different host species. Furthermore, we pairedC. coligenomic information and LOS chemical composition for the first time to investigate possible associations between LOS locus class sequence diversity and biochemical heterogeneity. After identifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structural heterogeneity. Mass spectrometry analysis of the LOSs of nine isolates, representing four different LOS classes, identified two features distinguishingC. coliLOS from that ofCampylobacter jejuni. 2-Amino-2-deoxy-d-glucose (GlcN)–GlcN disaccharides were present in the lipid A backbone, in contrast to the β-1′-6-linked 3-diamino-2,3-dideoxy-d-glucopyranose (GlcN3N)–GlcN backbone observed inC. jejuni. Moreover, despite the fact that many of the genes putatively involved in 3-acylamino-3,6-dideoxy-d-glucose (Quip3NAcyl) were apparently absent from the genomes of various isolates, this rare sugar was found in the outer core of allC. coliisolates. Therefore, regardless of the high genetic diversity of the LOS biosynthesis locus inC. coli, we identified species-specific phenotypic features ofC. coliLOS that might explain differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.IMPORTANCEDespite the importance ofC. colito human health and its controversial role as a causative agent of Guillain-Barré syndrome, little is known about the genetic and phenotypic diversity ofC. coliLOSs. Therefore, we pairedC. coligenomic information and LOS chemical composition for the first time to address this paucity of information. We identified two species-specific phenotypic features ofC. coliLOS, which might contribute to elucidating the reasons behind the differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.

scholarly journals Unlocking the Diversity of Pyrroloiminoquinones Produced by Latrunculid Sponge Species

Marine Drugs ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 68
Author(s):  
Jarmo-Charles J. Kalinski ◽  
Rui W. M. Krause ◽  
Shirley Parker-Nance ◽  
Samantha C. Waterworth ◽  
Rosemary A. Dorrington
Keyword(s):  
New Species ◽  
Secondary Metabolites ◽  
Distinct Species ◽  
Collision Induced Dissociation ◽  
Specific Chemical ◽  
Organic Extracts ◽  
Chemical Profiles ◽  
Species Specific ◽  
Related Compounds ◽  
Sulfur Containing

Sponges of the Latrunculiidae family produce bioactive pyrroloiminoquinone alkaloids including makaluvamines, discorhabdins, and tsitsikammamines. The aim of this study was to use LC-ESI-MS/MS-driven molecular networking to characterize the pyrroloiminoquinone secondary metabolites produced by six latrunculid species. These are Tsitsikamma favus, Tsitsikamma pedunculata, Cyclacanthia bellae, and Latrunculia apicalis as well as the recently discovered species, Tsitsikamma nguni and Tsitsikamma michaeli. Organic extracts of 43 sponges were analyzed, revealing distinct species-specific chemical profiles. More than 200 known and unknown putative pyrroloiminoquinones and related compounds were detected, including unprecedented makaluvamine-discorhabdin adducts and hydroxylated discorhabdin I derivatives. The chemical profiles of the new species T. nguni closely resembled those of the known T. favus (chemotype I), but with a higher abundance of tsitsikammamines vs. discorhabdins. T. michaeli sponges displayed two distinct chemical profiles, either producing mostly the same discorhabdins as T. favus (chemotype I) or non- or monobrominated, hydroxylated discorhabdins. C. bellae and L. apicalis produced similar pyrroloiminoquinone chemistry to one another, characterized by sulfur-containing discorhabdins and related adducts and oligomers. This study highlights the variability of pyrroloiminoquinone production by latrunculid species, identifies novel isolation targets, and offers fundamental insights into the collision-induced dissociation of pyrroloiminoquinones.

scholarly journals Metazoan ribotoxin genes acquired by Horizontal Gene Transfer

2016 ◽  
Author(s):  
Walter J. Lapadula ◽  
Paula L. Marcet ◽  
María L. Mascotti ◽  
María V. Sánchez Puerta ◽  
Maximiliano Juri Ayub
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Species ◽  
Purifying Selection ◽  
28S Rrna ◽  
Closely Related Species ◽  
Functional Roles ◽  
Ribosome Inactivating Proteins ◽  
First Time ◽  
Encoding Genes

AbstractRibosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that the culicine RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a Cyanobacterial donor species. Moreover, evolutionary analyses show that, after transference, these genes evolved under purifying selection, strongly suggesting that they play functional roles in these organisms. In this work we confirm the presence of RIP genes in Culicinae species, and show solid evidence supporting the hypothesis that these genes are derived from a single prokaryotic transferred gene through HGT. In addition, clear evidence of purifying selection pressure has been recorded, supporting the hypothesis that these genes are functional within this subfamily.

scholarly journals Evolution of co-regulatory network of C4 metabolic genes and TFs in the genus Flaveria: go anear or away in the intermediate species?

2020 ◽  
Author(s):  
Ming-Ju Amy Lyu ◽  
Jemaa Essemine ◽  
Faming Chen ◽  
Genyun Chen ◽  
Xin-Guang Zhu
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Evolutionary Process ◽  
Type I ◽  
Type Ii ◽  
Intermediate Species ◽  
Closely Related Species ◽  
Metabolic Genes ◽  
Species Specific ◽  
First Time

AbstractC4 photosynthesis evolved from the ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 photosynthesis have been intensively studied; however, the transcription factors (TFs) regulating these C4 metabolic genes are not well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolution is unclear. Here, we constructed TFs co-regulatory networks for core C4 metabolic genes (C4GRN) for four evolutionarily closely related species from the genus Flaveria, which represent four different evolutionary stages of the C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that more than half of the co-regulations of TFs and C4 core metabolic genes were species specific. The counterparts of C4 genes in C3 species were already co-regulated with the photosynthesis-related genes; whereas the required TFs for the C4 photosynthesis were recruited later. The type I C3-C4 species recruited 40% of C4 required TFs which co-regulated all core C4 metabolic genes but PEPC; nevertheless, the type II C3-C4 species took on a high divergent C4GRN with C4 species itself. In C4 species, PEPC and PPDK-RP possessed much more co-regulated TFs than other C4 metabolic genes. This study provides for the first time the TFs profiles of the C4 metabolic genes in species with different photosynthetic types and reveal the dynamic of C4 genes-TFs co-regulations along the evolutionary process, providing thereby new insights into the evolution of C4 photosynthesis.

scholarly journals Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan

2015 ◽  
Vol 197 (9) ◽  
pp. 1538-1548 ◽  
Author(s):  
Varsha Raghavan ◽  
Eduardo A. Groisman
Keyword(s):  
Chondroitin Sulfate ◽  
Related Species ◽  
Bacterial Species ◽  
Nutrient Utilization ◽  
Gut Bacteria ◽  
Dynamic Responses ◽  
Microbial Composition ◽  
Specific Expression ◽  
Content Type ◽  
Species Specific

ABSTRACTThe mammalian intestine provides nutrients to hundreds of bacterial species. Closely related species often harbor homologous nutrient utilization genes and cocolonize the gut, raising questions regarding the strategies mediating their stable coexistence. Here we reveal that relatedBacteroidesspecies that can utilize the mammalian glycan chondroitin sulfate (CS) have diverged in the manner in which they temporally regulate orthologous CS utilization genes. Whereas certainBacteroidesspecies display a transient surge in CS utilization transcripts upon exposure to CS, other species exhibit sustained activation of these genes. Remarkably, species-specific expression dynamics are retained even when the key players governing a particular response are replaced by those from a species with a dissimilar response.Bacteroidesspecies exhibiting distinct expression behaviors in the presence of CS can be cocultured on CS. However, they vary in their responses to CS availability and to the composition of the bacterial community when CS is the sole carbon source. Our results indicate that diversity resulting from regulation of polysaccharide utilization genes may enable the coexistence of gut bacterial species using a given nutrient.IMPORTANCEGenes mediating a specific task are typically conserved in related microbes. For instance, gutBacteroidesspecies harbor orthologous nutrient breakdown genes and may face competition from one another for these nutrients. How, then, does the gut microbial composition maintain such remarkable stability over long durations? We establish that in the case of genes conferring the ability to utilize the nutrient chondroitin sulfate (CS), microbial species vary in how they temporally regulate these genes and exhibit subtle growth differences on the basis of CS availability and community composition. Similarly to how differential regulation of orthologous genes enables related species to access new environments, gut bacteria may regulate the same genes in distinct fashions to reduce the overlap with coexisting species for utilization of available nutrients.

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