The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors

ABSTRACT Teleost fish represent the most diverse of the vertebrate groups and play important roles in food webs, as ecosystem engineers, and as vectors for microorganisms. However, the microbial ecology of fishes remains underexplored for most host taxa and for certain niches on the fish body. This is particularly true for the gills, the key sites of respiration and waste exchange in fishes. Here we provide a comprehensive analysis of the gill microbiome. We focus on ecologically diverse taxa from coral reefs around Moorea, sampling the gills and intestines of adults and juveniles representing 15 families. The gill microbiome composition differed significantly from that of the gut for both adults and juveniles, with fish-associated niches having lower alpha diversity values and higher beta diversity values than those for seawater, sediment, and alga-associated microbiomes. Of ∼45,000 operational taxonomic units (OTUs) detected across all samples, 11% and 13% were detected only in the gill and the intestine, respectively. OTUs most enriched in the gill included members of the gammaproteobacterial genus Shewanella and the family Endozoicimonaceae . In adult fish, both gill and intestinal microbiomes varied significantly among host species grouped by diet category. Gill and intestinal microbiomes from the same individual were more similar to one another than to gill and intestinal microbiomes from different individuals. These results demonstrate that distinct body sites are jointly influenced by host-specific organizing factors operating at the level of the host individual. The results also identify taxonomic signatures unique to the gill and the intestine, confirming fish-associated niches as distinct reservoirs of marine microbial diversity. IMPORTANCE Fish breathe and excrete waste through their gills. The gills are also potential sites of pathogen invasion and colonization by other microbes. However, we know little about the microbial communities that live on the gill and the factors shaping their diversity. Focusing on ecologically distinct types of coral reef fish, we provide a comprehensive analysis of the fish gill microbiome. By comparison to microbiomes of the gut and the surrounding environment, we identify microbes unique to the gill niche. These microbes may be targets for further studies to determine the contribution of the microbiome to waste exchange or host immunity. We also show that despite exhibiting a unique taxonomic signature, the gill microbiome is influenced by factors that also influence the gut microbiome. These factors include the specific identity of the host individual. These results suggest basic principles describing how association with fishes structures the composition of microbial communities.

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Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

mBio ◽

10.1128/mbio.00145-21 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Lauren E. Fuess ◽

Stijn den Haan ◽

Fei Ling ◽

Jesse N. Weber ◽

Natalie C. Steinel ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Gut Microbiome ◽

Alpha Diversity ◽

Host Immunity ◽

Host Gene ◽

Microbiota Composition ◽

Host Gene Expression ◽

Microbiome Composition ◽

Immune Genes

ABSTRACT Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions, as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However, few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here, we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immune genes. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated with host gene expression. These families were all tightly correlated with host expression of immune genes and processes, falling into one of three categories—those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with the abundance of these taxa, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition. IMPORTANCE Here, we document associations between host gene expression and gut microbiome composition in a nonmammalian vertebrate species. We highlight associations between expression of immune genes and both microbiome diversity and abundance of specific microbial taxa. These findings support other findings from model systems which have suggested that gut microbiome composition and host immunity are intimately linked. Furthermore, we demonstrate that these correlations are truly systemic; the gene expression detailed here was collected from an important fish immune organ (the head kidney) that is anatomically distant from the gut. This emphasizes the systemic impact of connections between gut microbiota and host immune function. Our work is a significant advancement in the understanding of immune-microbiome links in nonmodel, natural systems.

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Immune gene expression covaries with gut microbiome composition in stickleback

10.1101/2020.08.04.236786 ◽

2020 ◽

Author(s):

Lauren Fuess ◽

Stijn den Haan ◽

Fei Ling ◽

Jesse N. Weber ◽

Natalie C. Steinel ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Gut Microbiome ◽

Alpha Diversity ◽

Host Immunity ◽

Host Gene ◽

Microbiota Composition ◽

Host Gene Expression ◽

Microbiome Composition ◽

Immune Genes

ABSTRACTCommensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immunity. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated to host gene expression. These families were all tightly correlated to host expression of immune genes and processes, falling into one of three categories: those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with abundance of these taxons, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition.

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Dietary Patterns and Gut Microbiome Composition in a Large Population-Based Cohort

Current Developments in Nutrition ◽

10.1093/cdn/nzaa046_014 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 514-514

Author(s):

Zhangling Chen ◽

Djawad Radjabzadeh ◽

Arfan Ikram ◽

Andre Uitterlinden ◽

Robert Kraaij ◽

...

Keyword(s):

Microbial Communities ◽

Diet Quality ◽

Gut Microbiome ◽

Linear Models ◽

Large Population ◽

Alpha Diversity ◽

Population Based ◽

Shannon Index ◽

Food Groups ◽

Microbiome Composition

Abstract Objectives Effects of diet on health and disease risk may be mediated by changes in gut microbiome composition. Our aim was to examine associations between intake of food groups and overall diet quality with gut microbiome composition in a large population-based cohort. Methods We analyzed data of 1130 participants (median age 57 years) from the Rotterdam Study, a population-based cohort study in the Netherlands. We measured dietary intake using a 389-item FFQ, and assessed adherence to dietary guidelines for 14 food groups and combined into a diet quality score. We assessed gut microbiome composition using 16S rRNA gene sequencing. Data were available for 11 phyla, 19 classes, 25 orders, 44 families, and 184 genera. Alpha diversity was quantified by Shannon index and Richness, and beta diversity was qualified by Bray-Curtis distance. We used linear models to examine associations with Shannon index and Richness, Adonis function to examine variations of Bray-Curtis distance, and Multivariate Association with Linear Models to examine associations with gut microbial communities. Models were adjusted for technical covariates, energy intake, age, sex, physical activity, education, smoking and BMI. Results After adjustment, higher diet quality was associated with more alpha diversity and explained part of the variation in beta diversity (P < 0.001). Overall diet quality was associated with relative abundance of four families (Erysipelotrichaceae, Ruminococcaceae, Lachnospiraceae, Christensenellaceae), and 15 genera (Torques group, RuminococcaceaeUCG002, RuminococcaceaeUCG003, RuminococcaceaeUCG005, RuminococcaceaeUCG010, Xylanophilum group, Blautia, RuminococcaceaeNK4A214 group, Eligens group, Coprococcus3, Senegalimassilia, Lachnospira, Halliigroup, ChristensenellaceaeR7 group, Ventriosum group) (adjusted p: q < 0.05). Results were not explained by any single food group. Higher intake of fruits, vegetables, whole grains, and tea, and lower intake of red meat and alcohol were all related to microbiome composition. Replication analyses are ongoing. Conclusions Better overall diet quality may improve overall gut microbial diversity. Furthermore, diet quality may influence abundance of certain gut microbial communities, several of which have previously been linked to lower risk of metabolic and inflammatory diseases. Funding Sources N/A.

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Rumen bacterial community of young and adult of reindeer (Rangifer tarandus) from Yamalo-Nenets Autonomous District of Russia

Open Agriculture ◽

10.1515/opag-2020-0001 ◽

2020 ◽

Vol 5 (1) ◽

pp. 10-20 ◽

Cited By ~ 1

Author(s):

Kasim A. Laishev ◽

Larisa A. Ilina ◽

Valentina A. Filippova ◽

Timur P. Dunyashev ◽

Georgiy Yu. Laptev ◽

...

Keyword(s):

Microbial Communities ◽

Rangifer Tarandus ◽

Biological Diversity ◽

Physiological State ◽

Alpha Diversity ◽

Operational Taxonomic Unit ◽

Taxonomic Composition ◽

Food Material ◽

Alpha And Beta Diversity ◽

Microbiome Composition

AbstractThe aim of the work was to compare the taxonomic composition of the rumen procariotic community in young and adult individuals of Nenets breed reindeer (Rangifer tarandus ) from the central part of the Yamal region by using the NGS method (next generation sequencing) and compare the microbiome composition of reindeer with the microbiome of their initial vegetation food material. The obtained data showed that the dominant position in microbial communities, like that of other ruminants, was occupied by representatives of phylum Firmicutes and Bacteroidetes, whose total share between observed groups did not differ significantly. The composition of the microbiome of the rumen of the investigated group of animals was completely different from the microbiome structure of the initial vegetation cover. Digestion of vegetation by reindeers resulted in complex transformation in the initial plant microbiome and an increase of biological diversity which was expressed in operational taxonomic unit (OTU) numbers increasing and changes in indexes of alpha-diversity parameters. According to the results of alpha- and beta- diversity of the rumen microbial communities, the greatest uniqueness was revealed for the microbiomes of the adults in comparison with calves and young. The presence of changes in the biodiversity indexes of the rumen microbiota in the reindeer, examined by us, confirm the opinion of the researchers that the microbial community may also reflect the physiological state of the animals. It has also been demonstrated that the presence of the phylum Verrucomicrobia, and the genera Stenotrophomonas, Pseudomonas, etc., may be specific to Nenets breed reindeer and have a pattern with their presence on various plants and lichens that are part of the reindeer diet. This is partially confirmed by data on plants microbiome taxonomy.

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Bacterial Community Dynamics across the Gastrointestinal Tracts of Dairy Calves during Preweaning Development

Applied and Environmental Microbiology ◽

10.1128/aem.02675-17 ◽

2018 ◽

Vol 84 (9) ◽

pp. e02675-17 ◽

Cited By ~ 16

Author(s):

Juliana Dias ◽

Marcos Inácio Marcondes ◽

Shirley Motta de Souza ◽

Barbara Cardoso da Mata e Silva ◽

Melline Fontes Noronha ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Early Life ◽

Community Dynamics ◽

Temporal Dynamics ◽

Alpha Diversity ◽

Dairy Calves ◽

Dairy Calf ◽

Content Type ◽

Bacterial Community Dynamics

ABSTRACTMicrobial communities play critical roles in the gastrointestinal tracts (GIT) of preruminant calves by influencing performance and health. However, little is known about the establishment of microbial communities in the calf GIT or their dynamics during development. In this study, next-generation sequencing was used to assess changes in the bacterial communities of the rumen, jejunum, cecum, and colon in 26 crossbred calves at four developmental stages (7, 28, 49, and 63 days old). Alpha diversity differed among GIT regions with the lowest diversity and evenness in the jejunum, whereas no changes in alpha diversity were observed across developmental stage. Beta diversity analysis showed both region and age effects, with low numbers of operational taxonomic units (OTUs) shared between regions within a given age group or between ages in a given region. Taxonomic analysis revealed that several taxa coexisted in the rumen, jejunum, cecum, and colon but that their abundances differed considerably by GIT region and age. As calves aged, we observed lower abundances of taxa such asBacteroides,Parabacteroides, andParaprevotellawith higher abundances ofBulleidiaandSucciniclasticumin the rumen. The jejunum also displayed taxonomic changes with increases inClostridiaceaeandTuricibactertaxa in older calves. In the lower gut, taxa such asLactobacillus,Blautia, andFaecalibacteriumdecreased and S24-7,Paraprevotella, andPrevotellaincreased as calves aged. These data support a model whereby early and successive colonization by bacteria occurs across the GIT of calves and provides insights into the temporal dynamics of the GIT microbiota of dairy calves during preweaning development.IMPORTANCEThe gastrointestinal tracts (GIT) of ruminants, such as dairy cows, house complex microbial communities that contribute to their overall health and support their ability to produce milk. For example, the rumen microbiota converts feed into usable nutrients, while the jejunal microbiota provides access to protein. Thus, establishing a properly functioning GIT microbiota in dairy calves is critical to their productivity as adult cows. However, little is known about the establishment, maintenance, and dynamics of the calf GIT microbiota in early life. In this study, we evaluated the bacterial communities in the rumen, jejunum, cecum, and colon in dairy calves across preweaning development and show that they are highly variable early on in life before transitioning to a stable community. Understanding the dairy calf GIT microbiota has implications for ensuring proper health during early life and will aid in efforts to develop strategies for improving downstream production.

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A gene co-association network regulating gut microbial communities in a Duroc pig population

Microbiome ◽

10.1186/s40168-020-00994-8 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Antonio Reverter ◽

Maria Ballester ◽

Pamela A. Alexandre ◽

Emilio Mármol-Sánchez ◽

Antoni Dalmau ◽

...

Keyword(s):

Microbial Communities ◽

Candidate Genes ◽

Relative Abundance ◽

Association Studies ◽

Single Gene ◽

Host Genome ◽

Genome Wide Association Studies ◽

Vaccine Response ◽

Microbiome Composition ◽

Host Genetic

Abstract Background Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical “single-gene-single-trait” approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. Results In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP–P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. Conclusions Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits.

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Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Pathogens ◽

10.3390/pathogens10040405 ◽

2021 ◽

Vol 10 (4) ◽

pp. 405

Author(s):

Anna Matysiak ◽

Michal Kabza ◽

Justyna A. Karolak ◽

Marcelina M. Jaworska ◽

Malgorzata Rydzanicz ◽

...

Keyword(s):

Microbial Communities ◽

Ocular Surface ◽

Molecular Techniques ◽

Corneal Tissue ◽

Rna Seq ◽

Microbiome Composition ◽

Viral Sequences ◽

Pcr Techniques ◽

Unmapped Reads

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

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Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

mBio ◽

10.1128/mbio.01851-20 ◽

2020 ◽

Vol 11 (4) ◽

Author(s):

Andrew Oliver ◽

Brandon LaMere ◽

Claudia Weihe ◽

Stephen Wandro ◽

Karen L. Lindsay ◽

...

Keyword(s):

Mass Spectrometry ◽

Reproductive Health ◽

Microbial Communities ◽

Carbon Sources ◽

Amplicon Sequencing ◽

Vaginal Microbiome ◽

Content Type ◽

Healthy Women ◽

Healthy Pregnancy ◽

Tof Ms

ABSTRACT Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition. IMPORTANCE Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

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Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

Applied and Environmental Microbiology ◽

10.1128/aem.03001-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 177-183 ◽

Cited By ~ 10

Author(s):

Lavane Kim ◽

Eulyn Pagaling ◽

Yi Y. Zuo ◽

Tao Yan

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Bacterial Species ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Content Type ◽

Property Change ◽

And Control ◽

Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity

mBio ◽

10.1128/mbio.01520-15 ◽

2015 ◽

Vol 6 (6) ◽

Cited By ~ 26

Author(s):

Kyle C. Costa ◽

Megan Bergkessel ◽

Scott Saunders ◽

Jonas Korlach ◽

Dianne K. Newman

Keyword(s):

Microbial Communities ◽

Pathogenic Fungi ◽

Cell Types ◽

Redox Activity ◽

Mycobacterium Fortuitum ◽

Active Metabolites ◽

Content Type ◽

Phenazine Production ◽

Physiological Benefits

ABSTRACTDiverse bacteria, including severalPseudomonasspecies, produce a class of redox-active metabolites called phenazines that impact different cell types in nature and disease. Phenazines can affect microbial communities in both positive and negative ways, where their presence is correlated with decreased species richness and diversity. However, little is known about how the concentration of phenazines is modulatedin situand what this may mean for the fitness of members of the community. Through culturing of phenazine-degrading mycobacteria, genome sequencing, comparative genomics, and molecular analysis, we identified several conserved genes that are important for the degradation of threePseudomonas-derived phenazines: phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), and pyocyanin (PYO). PCA can be used as the sole carbon source for growth by these organisms. Deletion of several genes inMycobacterium fortuitumabolishes the degradation phenotype, and expression of two genes in a heterologous host confers the ability to degrade PCN and PYO. In cocultures with phenazine producers, phenazine degraders alter the abundance of different phenazine types. Not only does degradation support mycobacterial catabolism, but also it provides protection to bacteria that would otherwise be inhibited by the toxicity of PYO. Collectively, these results serve as a reminder that microbial metabolites can be actively modified and degraded and that these turnover processes must be considered when the fate and impact of such compounds in any environment are being assessed.IMPORTANCEPhenazine production byPseudomonasspp. can shape microbial communities in a variety of environments ranging from the cystic fibrosis lung to the rhizosphere of dryland crops. For example, in the rhizosphere, phenazines can protect plants from infection by pathogenic fungi. The redox activity of phenazines underpins their antibiotic activity, as well as providing pseudomonads with important physiological benefits. Our discovery that soil mycobacteria can catabolize phenazines and thereby protect other organisms against phenazine toxicity suggests that phenazine degradation may influence turnoverin situ. The identification of genes involved in the degradation of phenazines opens the door to monitoring turnover in diverse environments, an essential process to consider when one is attempting to understand or control communities influenced by phenazines.

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