RESUMO
Bacteroides species are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-ß-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron. Examining the genomes of other Bacteroides species, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.
RESUMO
The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.
RESUMO
Lineage specific expansions and gene duplications are some of the most important sources of evolutionary novelty in eukaryotes. Although not as prevalent in eukaryotes compared to bacteria, horizontal gene transfer events can also result in key adaptations for insects, especially for those involved in insect-microbe interactions. In this study we assemble the first chromosomal assembly of the psyllid Bactericera cockerelli and reveal that the B. cockerelli genome has experienced significantly more gene expansion events compared to other Hemipteran representatives with fully sequenced genomes. We also reveal that B. cockerelli's genome is the largest psyllid genome (567 Mb) sequenced to date and is ~15% larger than the other two psyllid species genomes sequenced (Pachypsylla venusta and Diaphorina citri). Structurally, B. cockerelli appears to have an additional chromosome compared to the distantly related psyllid species P. venusta due to a previous chromosomal fission or fusion event. The increase in genome size and dynamic nature of the B. cockerelli genome may largely be contributed to the widespread expansion of type I and II repeat elements that are rampant across all of B. cockerelli's. chromosomes. These repeat elements are distributed near equally in both euchromatic and heterochromatic regions. Furthermore, significant gene family expansions and gene duplications were uncovered for genes that are expected to be important in its adaptation to insect-plant and microbe interactions, which include transcription factors, proteases, odorant receptors, and horizontally transferred genes that are involved in the nutritional symbioses with their long-term nutritional endosymbiont Carsonella.
Assuntos
Hemípteros , Animais , Hemípteros/genética , Simbiose/genética , Genoma , Bactérias/genética , CromossomosRESUMO
SignificanceIn a polymicrobial battlefield where different species compete for nutrients and colonization niches, antimicrobial compounds are the sword and shield of commensal microbes in competition with invading pathogens and each other. The identification of an Escherichia coli-produced genotoxin, colibactin, and its specific targeted killing of enteric pathogens and commensals, including Vibrio cholerae and Bacteroides fragilis, sheds light on our understanding of intermicrobial interactions in the mammalian gut. Our findings elucidate the mechanisms through which genotoxins shape microbial communities and provide a platform for probing the larger role of enteric multibacterial interactions regarding infection and disease outcomes.
Assuntos
Cólera/microbiologia , Microbioma Gastrointestinal , Interações Hospedeiro-Patógeno , Interações Microbianas , Mutagênicos/metabolismo , Vibrio cholerae/fisiologia , Animais , Antibiose , Cólera/mortalidade , Dano ao DNA , Modelos Animais de Doenças , Escherichia coli/fisiologia , Humanos , Camundongos , Peptídeos/metabolismo , Peptídeos/farmacologia , Policetídeos/metabolismo , Policetídeos/farmacologia , Prognóstico , Espécies Reativas de Oxigênio , Vibrio cholerae/efeitos dos fármacosRESUMO
The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes beneficial for their host's self-defense (e.g., antibiotic resistance) or ability to compete for essential or limited resources (e.g., vitamins). Vitamin B12 and related compounds (corrinoids) are critical nutrients that enable colonization by members of the common gut microbe phylum, the Bacteroidetes. Herein, we identify a distinct class of MGEs in the Bacteroidetes responsible for the mobilization and exchange of the genes required for transport of corrinoids, a group of cyclic tetrapyrrole cofactors including vitamin B12 (btuGBFCD). This class includes two distinct groups of conjugative transposons (CTns) and one group of phage. Conjugative transfer and vitamin B12 transport activity of two of the CTns were confirmed in vitro and in vivo, demonstrating the important role MGEs play in distribution of corrinoid transporters in the Bacteroidetes.
Assuntos
Proteínas de Bactérias/metabolismo , Bacteroidetes/metabolismo , Corrinoides/metabolismo , Microbioma Gastrointestinal , Sequências Repetitivas Dispersas , Proteínas de Membrana Transportadoras/metabolismo , Vitamina B 12/metabolismo , Animais , Proteínas de Bactérias/genética , Bacteroidetes/crescimento & desenvolvimento , Feminino , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Complexo Vitamínico B/metabolismoRESUMO
Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here, we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in many Bacteroides species. A purified RBP, RbpB, from Bacteroides thetaiotaomicron binds to single-stranded RNA in vitro with an affinity similar to other characterized regulatory RBPs. B. thetaiotaomicron mutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. A B. thetaiotaomicron ΔrbpB mutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpB mutant had reduced expression of BT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation of BT1871 confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression of BT1871 and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes. IMPORTANCE The human colon houses hundreds of bacterial species, including many belonging to the genus Bacteroides, that aid in breaking down our food to keep us healthy. Bacteroides have many genes responsible for breaking down different dietary carbohydrates, and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered that Bacteroides use a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical for Bacteroides to live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.
Assuntos
Proteínas de Bactérias/metabolismo , Bacteroides thetaiotaomicron/metabolismo , Regulação Bacteriana da Expressão Gênica/fisiologia , Polissacarídeos Bacterianos/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteínas de Bactérias/genética , Bacteroides thetaiotaomicron/genética , Humanos , Proteínas de Ligação a RNA/genéticaRESUMO
Historically it has been difficult to study the evolution of bacterial small RNAs (sRNAs) across distantly related species. For example, identifying homologs of sRNAs is often difficult in genomes that have undergone multiple structural rearrangements. Also, some types of regulatory sRNAs evolve at rapid rates. The high degree of genomic synteny among divergent host-restricted bacterial lineages, including intracellular symbionts, is conducive to sRNA maintenance and homolog identification. In turn, symbiont genomes can provide us with novel insights into sRNA evolution. Here, we examine the sRNA expression profile of the obligate symbiont of psyllids, Carsonella ruddii, which has one of the smallest cellular genomes described. Using RNA-seq, we identified 36 and 32 antisense sRNAs (asRNAs) expressed by Carsonella from the psyllids Bactericera cockerelli (Carsonella-BC) and Diaphorina citri (Carsonella-DC), respectively. The majority of these asRNAs were associated with genes that are involved in essential amino acid biosynthetic pathways. Eleven of the asRNAs were conserved in both Carsonella lineages and the majority were maintained by selection. Notably, five of the corresponding coding sequences are also the targets of conserved asRNAs in a distantly related insect symbiont, Buchnera. We detected differential expression of two asRNAs for genes involved in arginine and leucine biosynthesis occurring between two distinct Carsonella-BC life stages. Using asRNAs identified in Carsonella, Buchnera, and Profftella which are all endosymbionts, and Escherichia coli, we determined that regions upstream of these asRNAs encode unique conserved patterns of AT/GC richness, GC skew, and sequence motifs which may be involved in asRNA regulation.
Assuntos
Buchnera , Hemípteros , Animais , Buchnera/genética , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano , Hemípteros/genética , RNA Bacteriano/genética , Seleção Genética , Simbiose/genéticaRESUMO
Gut-associated phages are hypothesized to alter the abundance and activity of their bacterial hosts, contributing to human health and disease. Although temperate phages constitute a significant fraction of the gut virome, the effects of lysogenic infection are underexplored. We report that the temperate phage, Bacteroides phage BV01, broadly alters its host's transcriptome, the prominent human gut symbiont Bacteroides vulgatus. This alteration occurs through phage-induced repression of a tryptophan-rich sensory protein (TspO) and represses bile acid deconjugation. Because microbially modified bile acids are important signals for the mammalian host, this is a mechanism by which a phage may influence mammalian phenotypes. Furthermore, BV01 and its relatives in the proposed phage family Salyersviridae are ubiquitous in human gut metagenomes, infecting a broad range of Bacteroides hosts. These results demonstrate the complexity of phage-bacteria-mammal relationships and emphasize a need to better understand the role of temperate phages in the gut microbiome.
Assuntos
Bacteriófagos/fisiologia , Bacteroides/genética , Bacteroides/virologia , Ácidos e Sais Biliares/metabolismo , Microbioma Gastrointestinal/genética , Interações Hospedeiro-Patógeno/genética , Transcriptoma/genética , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bacteriófagos/genética , Genoma Viral , Humanos , Lisogenia , Camundongos Endogâmicos C57BL , Filogenia , Regiões Promotoras Genéticas/genética , Transcrição GênicaRESUMO
Small RNAs (sRNAs) posttranscriptionally regulate mRNA targets, typically under conditions of environmental stress. Although hundreds of sRNAs have been discovered in diverse bacterial genomes, most sRNAs remain uncharacterized, even in model organisms. Identification of mRNA targets directly regulated by sRNAs is rate-limiting for sRNA functional characterization. To address this, we developed a computational pipeline that we named SPOT for sRNA target prediction organizing tool. SPOT incorporates existing computational tools to search for sRNA binding sites, allows filtering based on experimental data, and organizes the results into a standardized report. SPOT sensitivity (number of correctly predicted targets/number of total known targets) was equal to or exceeded any individual method when used on 12 characterized sRNAs. Using SPOT, we generated a set of target predictions for the sRNA RydC, which was previously shown to positively regulate cfa mRNA, encoding cyclopropane fatty acid synthase. SPOT identified cfa along with additional putative mRNA targets, which we then tested experimentally. Our results demonstrated that in addition to cfa mRNA, RydC also regulates trpE and pheA mRNAs, which encode aromatic amino acid biosynthesis enzymes. Our results suggest that SPOT can facilitate elucidation of sRNA target regulons to expand our understanding of the many regulatory roles played by bacterial sRNAs.IMPORTANCE Small RNAs (sRNAs) regulate gene expression in diverse bacteria by interacting with mRNAs to change their structure, stability, or translation. Hundreds of sRNAs have been identified in bacteria, but characterization of their regulatory functions is limited by difficulty with sensitive and accurate identification of mRNA targets. Thus, new robust methods of bacterial sRNA target identification are in demand. Here, we describe our small RNA target prediction organizing tool (SPOT), which streamlines the process of sRNA target prediction by providing a single pipeline that combines available computational prediction tools with customizable results filtering based on experimental data. SPOT allows the user to rapidly produce a prioritized list of predicted sRNA-target mRNA interactions that serves as a basis for further experimental characterization. This tool will facilitate elucidation of sRNA regulons in bacteria, allowing new discoveries regarding the roles of sRNAs in bacterial stress responses and metabolic regulation.
Assuntos
Bactérias/genética , Biologia Computacional/métodos , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos , RNA Bacteriano/genética , RNA Mensageiro/genética , Pequeno RNA não Traduzido/genética , Sítios de Ligação , Genética Microbiana/métodosRESUMO
Human gut Bacteroides use surface-exposed lipoproteins to bind and metabolize complex polysaccharides. Although vitamins and other nutrients are also essential for commensal fitness, much less is known about how commensal bacteria compete with each other or the host for these critical resources. Unlike in Escherichia coli, transport loci for vitamin B12 (cobalamin) and other corrinoids in human gut Bacteroides are replete with conserved genes encoding proteins whose functions are unknown. Here we report that one of these proteins, BtuG, is a surface-exposed lipoprotein that is essential for efficient B12 transport in B. thetaiotaomicron. BtuG binds B12 with femtomolar affinity and can remove B12 from intrinsic factor, a critical B12 transport protein in humans. Our studies suggest that Bacteroides use surface-exposed lipoproteins not only for capturing polysaccharides, but also to acquire key vitamins in the gut.
Assuntos
Bacteroides/metabolismo , Membrana Celular/metabolismo , Trato Gastrointestinal/microbiologia , Lipoproteínas/metabolismo , Vitamina B 12/metabolismo , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Transporte Biológico/genética , Corrinoides/metabolismo , Ligação Genética , Vida Livre de Germes , Humanos , Fator Intrínseco/metabolismo , Camundongos , Modelos Moleculares , Eletricidade EstáticaRESUMO
During infection, pathogens must obtain all inorganic nutrients, such as phosphate, from the host. Despite the essentiality of phosphate for all forms of life, how Staphylococcus aureus obtains this nutrient during infection is unknown. Differing from Escherichia coli, the paradigm for bacterial phosphate acquisition, which has two inorganic phosphate (Pi) importers, genomic analysis suggested that S. aureus possesses three distinct Pi transporters: PstSCAB, PitA, and NptA. While pitA and nptA are expressed in phosphate-replete media, expression of all three transporters is induced by phosphate limitation. The loss of a single transporter did not affect S. aureus However, disruption of any two systems significantly reduced Pi accumulation and growth in divergent environments. These findings indicate that PstSCAB, PitA, and NptA have overlapping but nonredundant functions, thus expanding the environments in which S. aureus can successfully obtain Pi Consistent with this idea, in a systemic mouse model of disease, loss of any one transporter did not decrease staphylococcal virulence. However, loss of NptA in conjunction with either PstSCAB or PitA significantly reduced the ability of S. aureus to cause infection. These observations suggest that Pi acquisition via NptA is particularly important for the pathogenesis of S. aureus While our analysis suggests that NptA homologs are widely distributed among bacteria, closely related less pathogenic staphylococcal species do not possess this importer. Altogether, these observations indicate that Pi uptake by S. aureus differs from established models and that acquisition of a third transporter enhances the ability of the bacterium to cause infection.
Assuntos
Proteínas de Bactérias/genética , Proteínas de Membrana Transportadoras/genética , Proteínas de Transporte de Fosfato/genética , Fosfatos/metabolismo , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/genética , Staphylococcus aureus/patogenicidade , Animais , Proteínas de Bactérias/metabolismo , Escherichia coli/genética , Feminino , Regulação Bacteriana da Expressão Gênica/genética , Camundongos , Camundongos Endogâmicos C57BL , Staphylococcus aureus/metabolismoRESUMO
Thiamine (vitamin B1) is an essential cofactor for all organisms. Humans primarily acquire thiamine through their diet, and thiamine deficiencies have adverse neurological effects. However, the role gut microbes play in modulating thiamine availability is poorly understood, and little is known about how thiamine impacts the stability of microbial gut communities. To investigate thiamine's role in the gut, we utilized the model gut microbe Bacteroides thetaiotaomicron. Transcriptome sequencing (RNA-seq) revealed a global downregulation of thiamine and amino acid biosynthesis, glycolysis, and purine metabolism when thiamine was present. Using genetic mutants with thiamine biosynthesis and transport locus mutations, we determined both systems were critical for growth in thiamine-deficient medium. The defect in the double transport mutant suggests an uncharacterized feedback mechanism between thiamine transport and biosynthesis in B. thetaiotaomicron. Mutant phenotypes were recapitulated during pairwise competitions, reinforcing the importance of encoding versatile thiamine acquisition mechanisms when thiamine concentrations are variable. In addition, liquid chromatography-mass spectrometry (LC-MS) analyses corroborate that exogenous thiamine levels affect the internal thiamine pool of B. thetaiotaomicron. Furthermore, we computationally examined the ability of other gut microbes to acquire thiamine and identified lineage-specific differences in thiamine acquisition strategies. Among the Bacteroidetes, the capacities for both thiamine transport and biosynthesis are common. Together, these data show that thiamine acquisition mechanisms used by B. thetaiotaomicron not only are critical for its physiology and fitness but also provide the opportunity to model how other gut microbes may respond to the shifting availability of thiamine in the gut. IMPORTANCE Variation in the ability of gut microbes to transport, synthesize, and compete for vitamin B1 (thiamine) is expected to impact the structure and stability of the microbiota, and ultimately this variation may have both direct and indirect effects on human health. Our study identifies the diverse strategies employed by gut Bacteroidetes to acquire thiamine. We demonstrate how the presence or absence of thiamine biosynthesis or transport dramatically affects the abundance of B. thetaiotaomicron in a competitive environment. This study adds further evidence that altering the presence or concentrations of water-soluble vitamins such as thiamine may be an effective method for manipulating gut community composition. In turn, targeted thiamine delivery could be used therapeutically to alter dysbiotic communities linked to disease. Author Video: An author video summary of this article is available.
RESUMO
The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate fundamental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities.
Assuntos
Trato Gastrointestinal/microbiologia , Microbiota , Vitamina B 12/metabolismo , Animais , Corrinoides/análise , Corrinoides/metabolismo , Trato Gastrointestinal/metabolismo , Humanos , Vitamina B 12/análiseRESUMO
Specific members of the intestinal microbiota dramatically affect inflammatory bowel disease (IBD) in mice. In humans, however, identifying bacteria that preferentially affect disease susceptibility and severity remains a major challenge. Here, we used flow-cytometry-based bacterial cell sorting and 16S sequencing to characterize taxa-specific coating of the intestinal microbiota with immunoglobulin A (IgA-SEQ) and show that high IgA coating uniquely identifies colitogenic intestinal bacteria in a mouse model of microbiota-driven colitis. We then used IgA-SEQ and extensive anaerobic culturing of fecal bacteria from IBD patients to create personalized disease-associated gut microbiota culture collections with predefined levels of IgA coating. Using these collections, we found that intestinal bacteria selected on the basis of high coating with IgA conferred dramatic susceptibility to colitis in germ-free mice. Thus, our studies suggest that IgA coating identifies inflammatory commensals that preferentially drive intestinal disease. Targeted elimination of such bacteria may reduce, reverse, or even prevent disease development.
Assuntos
Colite Ulcerativa/imunologia , Doença de Crohn/imunologia , Imunoglobulina A/imunologia , Microbiota , Animais , Colite Ulcerativa/microbiologia , Colite Ulcerativa/patologia , Doença de Crohn/microbiologia , Doença de Crohn/patologia , DNA Bacteriano/análise , Disbiose/imunologia , Disbiose/microbiologia , Humanos , Inflamassomos/imunologia , Inflamação/imunologia , Inflamação/microbiologia , Intestinos/imunologia , Intestinos/microbiologia , Camundongos , Camundongos Endogâmicos C57BL , RNA Ribossômico 16S/análise , Organismos Livres de Patógenos EspecíficosRESUMO
Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for â¼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.
Assuntos
Buchnera/genética , Genoma Bacteriano , Pequeno RNA não Traduzido/metabolismo , Simbiose/genética , Animais , Afídeos/microbiologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Buchnera/metabolismo , Regulação Bacteriana da Expressão Gênica , Biossíntese de Proteínas , RNA , Pequeno RNA não Traduzido/química , RNA não TraduzidoRESUMO
Genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. Whether these predictions reflect actual functional redundancies is unclear. We report that the prominent human gut symbiont Bacteroides thetaiotaomicron employs three functional, homologous vitamin B12 transporters that in at least two cases confer a competitive advantage in the presence of distinct B12 analogs (corrinoids). In the mammalian gut, microbial fitness can be determined by the presence or absence of a single transporter. The total number of distinct corrinoid transporter families in the human gut microbiome likely exceeds those observed in B. thetaiotaomicron by an order of magnitude. These results demonstrate that human gut microbes use elaborate mechanisms to capture and differentiate corrinoids in vivo and that apparent redundancies observed in these genomes can instead reflect hidden specificities that determine whether a microbe will colonize its host.
Assuntos
Proteínas da Membrana Bacteriana Externa/genética , Proteínas de Escherichia coli/genética , Trato Gastrointestinal/microbiologia , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano , Proteínas de Membrana Transportadoras/genética , Microbiota , Vitamina B 12/metabolismo , Animais , Antibiose/fisiologia , Proteínas da Membrana Bacteriana Externa/classificação , Proteínas da Membrana Bacteriana Externa/metabolismo , Bacteroides/genética , Bacteroides/metabolismo , Transporte Biológico , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/classificação , Proteínas de Escherichia coli/metabolismo , Humanos , Proteínas de Membrana Transportadoras/classificação , Proteínas de Membrana Transportadoras/metabolismo , Camundongos , Filogenia , Especificidade da Espécie , Simbiose/fisiologia , Vitamina B 12/análogos & derivadosRESUMO
The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities. These studies build upon, and are complemented by, experimental efforts to define underlying mechanisms of host-microbe interactions in simplified model systems. This review highlights the intersection of these approaches. Experimental studies now leverage the advances in high-throughput DNA sequencing that have driven the explosion of microbial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host-microbiota relationships and are readily applicable to other host-associated and free-living microbial communities.
Assuntos
Bactérias/genética , Trato Gastrointestinal/microbiologia , Metagenômica , Microbiota , Bactérias/isolamento & purificação , Bactérias/metabolismo , Humanos , Metagenoma , Metagenômica/métodosRESUMO
Microbes inhabiting the human gastrointestinal tract tend to adopt one of three characteristic community structures, called 'enterotypes', each of which is overrepresented by a distinct set of bacterial genera. Here we report that the gut microbiotae of chimpanzees also assort into enterotypes and that these chimpanzee enterotypes are compositionally analogous to those of humans. Through the analysis of longitudinal samples, we show that the microbial signatures of the enterotypes are stable over time, but that individual hosts switch between enterotypes over periods longer than a year. These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees.
Assuntos
Bactérias/isolamento & purificação , Trato Gastrointestinal/microbiologia , Pan troglodytes/microbiologia , Animais , Bactérias/classificação , Humanos , Fatores de TempoRESUMO
The gastrointestinal tract harbors large and diverse populations of bacteria that vary among individuals and within individuals over time. Numerous internal and external factors can influence the contents of these microbial communities, including diet, geography, physiology, and the extent of contact among hosts. To investigate the contributions of such factors to the variation and changes in gut microbial communities, we analyzed the distal gut microbiota of individual chimpanzees from two communities in Gombe National Park, Tanzania. These samples, which were derived from 35 chimpanzees, many of whom have been monitored for multiple years, provide an unusually comprehensive longitudinal depth for individuals of known genetic relationships. Although the composition of the great-ape microbiota has been shown to codiversify with host species, indicating that host genetics and phylogeny have played a major role in its differentiation over evolutionary timescales, the geneaological relationships of individual chimpanzees did not coincide with the similarity in their gut microbial communities. However, the inhabitants from adjacent chimpanzee communities could be distinguished based on the contents of their gut microbiota. Despite the broad similarity of community members, as would be expected from shared diet or interactions, long-term immigrants to a community often harbored the most distinctive gut microbiota, suggesting that individuals retain hallmarks of their previous gut microbial communities for extended periods. This pattern was reinforced in several chimpanzees sampled over long temporal scales, in which the major constituents of the gut microbiota were maintained for nearly a decade.
Assuntos
Evolução Biológica , Trato Gastrointestinal/microbiologia , Variação Genética , Pan troglodytes/microbiologia , Animais , Primers do DNA/genética , Fezes/microbiologia , Linhagem , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Estatísticas não Paramétricas , TanzâniaRESUMO
Microbes commonly exist in milieus of varying complexity and diversity. Although cultivation-based techniques have been unable to accurately capture the true diversity within microbial communities, these deficiencies have been overcome by applying molecular approaches that target the universally conserved 16S ribosomal RNA gene. The recent application of 454 pyrosequencing to simultaneously sequence thousands of 16S rDNA sequences (pyrotags) has revolutionized the characterization of complex microbial communities. To date, studies based on 454 pyrotags have dominated the field, but sequencing platforms that generate many more sequence reads at much lower costs have been developed. Here, we use the Illumina sequencing platform to design a strategy for 16S amplicon analysis (iTags), and assess its generality, practicality and potential complications. We fabricated and sequenced paired-end libraries of amplified hyper-variable 16S rDNA fragments from sets of samples that varied in their contents, ranging from a single bacterium to highly complex communities. We adopted an approach that allowed us to evaluate several potential sources of errors, including sequencing artifacts, amplification biases, non-corresponding paired-end reads and mistakes in taxonomic classification. By considering each source of error, we delineate ways to make biologically relevant and robust conclusions from the millions of sequencing reads that can be readily generated by this technology.