Host species as a strong determinant of the intestinal microbiota of fish larvae

We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.     

Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state-associated and mobile multidrug resistance-carrying bacteria

In agriculture, antibiotics are used for the treatment and prevention of livestock disease. Antibiotics perturb the bacterial gut composition but the extent of these changes and potential consequences for animal and human health is still debated. Six calves were housed in a controlled environment. Three animals received an injection of the antibiotic florfenicol (Nuflor), and three received no treatment. Faecal samples were collected at 0, 3 and 7 days, and bacterial communities were profiled to assess the impact of a therapy on the gut microbiota. Phylogenetic analysis (16S-rDNA) established that at day 7, antibiotic-treated microbiota showed a 10-fold increase in facultative anaerobic Escherichia spp, a signature of imbalanced microbiota, dysbiosis. The antibiotic resistome showed a high background of antibiotic resistance genes, which did not significantly change in response to florfenicol. However, the maintenance of Escherichia coli plasmid-encoded quinolone, oqxB and propagation of mcr-2, and colistin resistance genes were observed and confirmed by Sanger sequencing. The microbiota of treated animals was enriched with energy harvesting bacteria, common to obese microbial communities. We propose that antibiotic treatment of healthy animals leads to unbalanced, disease- and obese-related microbiota that promotes growth of E. coli carrying resistance genes on mobile elements, potentially increasing the risk of transmission of antibiotic resistant bacteria to humans.     

利福平对红裸须摇蚊幼虫肠道微生物群落结构及功能的潜在影响北大核心

【目的】摇蚊是水生生态系统中重要的昆虫种类之一,其肠道微生物与个体生长发育、环境适应等过程密切相关,本研究旨在探究抗生素处理对摇蚊幼虫肠道微生物群落结构及功能的潜在影响。【方法】利用16S rRNA基因扩增子测序技术对利福平处理的红裸须摇蚊(Propsilocerus akamusi)幼虫肠道内容物中的菌群进行分析和比较,应用Tax4Fun法对其肠道菌群功能进行预测。【结果】利福平处理能够改变红裸须摇蚊幼虫肠道群落结构和多样性,宿主肠道菌群中拟杆菌门(Bacteroidota)(P<0.05)以及脱铁杆菌门(Deferribacterota)(P<0.001)的相对丰度显著上升,而变形菌门(Proteobacteria)与厚壁菌门(Firmicutes)相对丰度有所下降。在属水平上,利福平处理使耶尔森菌属(Yersinia)、假单胞菌属(Pseudomonas)、脱硫弧菌属(Desulfovibrio)的相对丰度有所降低,其中脱硫弧菌属(Desulfovibrio)显著降低。与此同时,共线性网络分析表明利福平处理后细菌群落稳定性大幅下降,菌种之间关联性显著减弱。通过京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)通路注释预测出红裸须摇蚊幼虫肠道菌群基因与基因信息处理、新陈代谢、人类疾病等功能相关,利福平处理可以使肠道菌群基因的抗药性功能显著上升,而内分泌和代谢疾病功能显著下降。【结论】研究结果揭示了抗生素利福平对红裸须摇蚊幼虫肠道细菌群落结构及功能的潜在影响,为进一步探索摇蚊肠道菌群发挥的必要作用奠定理论基础。     

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses

Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture‐independent and ‐dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free‐range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.     

Comparison of gut microbiota of healthy and diseased walking sticks,Phasmotaenia lanyuhensis

Research on gut microbiota of phytophagous insects has shown to be important for the physiological functions of insect hosts; however, little is known about the changes in gut microbiota when they are suffering from environmental stress or pathogen infections. During rearing of Phasmotaenia lanyuhensis (Phasmatodea: Phasmatidae), sluggish locomotion was usually followed by the death of the insect with a symptom of melanization in the front part of the abdomen. Therefore, the abnormal individuals were initially classified into moribund, light- and serious-symptom based on the level of abnormal physiological circumstances and melanization. The gut microbiota of these samples were further investigated by 16S metagenomic sequencing and the differences in bacterial abundance and structure of bacterial community were analyzed. A decrease in microbiota diversity was observed in the diseased P. lanyuhensis, with the abundance of phyla Proteobacteria and Firmicute relatively higher compared to those without symptom. Interestingly, principal component analysis based on the bacterial richness was correlated to the level of melanization symptom in the diseased P. lanyuhensis, suggested the change in bacterial microbiota involved in this abnormal circumstance. However, the factor that caused the initial alternation of microbiota remains to be identified. Additionally, the lack of bacterial diversity (i.e., absence of Meiothermus and Nubsella spp.) in P. lanyuhensis might reduce the fitness for surviving. This report provided the comprehensive microbiota analysis for P. lanyuhensis and concluded that either the relative abundance or the bacterial diversity of microbiota in the insect digestive system may influence the physiological functions of phytophagous insects.     

The marine bivalve molluscs pathogen Vibrio neptunius produces the siderophore amphibactin,which is widespread in molluscs microbiota

Amphiphilic siderophores, including amphibactins, are the most abundant siderophores in oceans. Genes putatively encoding the amphibactin system were proposed in some bacteria and homologues of these genes are particularly abundant in multiple bacterial lineages inhabitant of low-iron seawater. However, since no defective mutant strains in any of these genes were studied to date, their role in amphibactin synthesis or uptake was not demonstrated. In this work, an in silico analysis of the genome of the mollusc pathogen Vibrio neptunius leads us to identify a gene cluster (denoted absABDEF) that is predicted to encode an amphibactin-like siderophore and several mutant strains unable to synthesize or use siderophores were constructed. The results showed that genes absABDEF are required for amphibactin synthesis. A comparative chemical analysis of V. neptunius wild type and biosynthesis mutants allowed us to identify a mixture of nine amphibactin forms produced by this bacterium. In addition, the gene abtA is predicted to encode the ferri-amphibactin outer membrane transporter. The prevalence of the amphibactin system in bivalve hemolymph microbiota was also studied. We found that the amphibactin system is widespread in hemolymph microbiota including both commensal and pathogenic bacterial species. Thus, its contribution to bacterial fitness must be more related to environmental persistence than to pathogenicity.     

The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities

The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species’ microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ‐proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation.     

Interspecific comparison of the fecal microbiota structure in three Arctic migratory bird species

The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink‐footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink‐footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink‐footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink‐footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink‐footed geese was discussed to be related with their herbivorous diet.     

银杏双黄酮和银杏内酯B与人体肠道菌群体外互作研究

【目的】银杏提取物在防治心血管系统和神经系统疾病方面发挥重要功能。鉴于肠道菌群已被认定为一个新兴的药物作用靶标,研究银杏双黄酮和银杏内酯与人体肠道菌群之间的相互作用具有非常重要的意义,这将为进一步理解银杏提取物的功能和作用机制奠定基础。【方法】本研究使用人体肠道菌群体外批量发酵、细菌总量测定、细菌16S rDNA高通量测序、气相色谱和液相色谱检测等方法,对银杏双黄酮和银杏内酯B单独或复合在体外与人体肠道菌群的相互作用进行研究。【结果】银杏双黄酮和银杏内酯B单独添加对人体肠道菌群总量、肠道菌群结构组成和短链脂肪酸产量没有显著影响。但有意思的是,复合添加银杏双黄酮和银杏内酯B后,Coriobacteriaceae科和Cupriavidus属细菌的比例显著升高,Gemella菌细菌比例显著降低。功能基因预测分析发现,编码K00076、K12143、K07716和K00220的基因在复合添加银杏双黄酮和银杏内酯B后显著富集。K00076和K00220是氧化还原酶,催化CH-OH供体基团的电子转移,可能参与银杏双黄酮和银杏内酯B的代谢和修饰。HPLC检测发现,人体肠道菌群体外对银杏双黄酮和银杏内脂B的降解修饰率分别为70%和35%左右。【结论】体外复合添加银杏双黄酮和银杏内酯B可显著改变肠道某些细菌的丰度。同时,体外研究表明肠道菌群具有代谢修饰银杏双黄酮和银杏内酯B的功能。     

Molecular analysis of the prevalent microbiota of human male and female forehead skin compared to forearm skin and the influence of make-up

Aims: To compare the bacterial diversity of two different ecological regions including human forehead, human forearm and to estimate the influence of make‐up. Methods and Results: Twenty‐two swab‐scraped skin samples were analysed by profiling bacterial 16S rRNA genes using PCR‐based sequencing of randomly selected clones. Of the 1056 clones analysed, 67 genera and 133 species‐level operational taxonomic units (SLOTUs) belonging to eight phyla were identified. A core set of bacterial taxa was found in all samples, including Actinobacteria, Firmicutes, and Proteobacteria, but pronounced intra‐ and interpersonal variation in bacterial community composition was observed. Only 4·48% of the genera and 1·50% of the SLOTUs were found in all 11 subjects. In contrast to the highly diverse microbiota of the forearm skin, the forehead skin microbiota represented a small‐scale ecosystem with a few genera found in all individuals. The use of make‐up, including foundation and powder, significantly enlarged the community diversity on the forehead skin. Conclusions: Our study confirmed the presence of a highly diverse microbiota of the human skin as described recently. In contrast to forearm skin, gender does not seem to have much influence on the microbial community of the forehead skin. However, the use of make‐up was associated with a remarkable increase in the bacterial diversity. Significance and Impact of the Study: This study enhances our knowledge about the highly complex microbiota of the human skin and demonstrates for the first time the significant effect of make‐up on the bacterial diversity of the forehead skin.     

Diversity and functional analysis of Chinese bumblebee gut microbiota reveal the metabolic niche and antibiotic resistance variation of Gilliamella

Bumblebees play an important role in maintaining the balance of natural and agricultural ecosystems,and the characteristic gut microbiota of bumblebees exhibit significant mutualistic functions.China has the highest diversity of bumblebees;however,gut microbiota of Chinese bumblebees have mostly been investigated through cultureindependent studies.Here,we analyzed the gut communities of bumblebees from Sichuan,Yunnan,and Shaanxi provinces in China through 16S ribosomal RNA amplicon sequencing and bacterial isolation.It revealed that the bumblebees examined in this study harbored two gut enterotypes as previously reported:one is dominated by Gilliamella and Snodgrassella,and the other is distinguished by prevalent environmental species.The gut compositions obviously varied among different individual bees.We then isolated 325 bacterial strains and the comparative genomic analysis of Gillianiella strains revealed that galactose and pectin digestion pathways were conserved in strains from bumblebees,while genes for the utilization of arabinose,mannose,xylose,and rhamnose were mostly lost.Only two strains from the Chinese bumblebees possess the multidrug-resistant gene emrB,which is phylogenetically closely related to that from the symbionts of soil entomopathogenic nematode.In contrast,tetracycline-resistant genes were uniquely present in three strains from the USA.Our results illustrate the prevalence of strain-level variations in the metabolic potentials and the distributions of antibiotic-resistant genes in Chinese bumblebee gut bacteria.     

The dissemination of C10 cysteine protease genes in <Emphasis Type="Italic">Bacteroides fragilis</Emphasis> by mobile genetic elements

Background  

The C10 family of cysteine proteases includes enzymes that contribute to the virulence of bacterial pathogens, such as SpeB in Streptococcus pyogenes. The presence of homologues of cysteine protease genes in human commensal organisms has not been examined. Bacteroides fragilis is a member of the dominant Bacteroidetes phylum of the human intestinal microbiota, and is a significant opportunistic pathogen.     

Plumage microbiota covaries with the major histocompatibility complex in blue petrels

To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odour remains largely unclear. MHC class IIB molecules, which enable recognition and elimination of extracellular bacteria, have been suggested to influence odour indirectly by shaping odour‐producing microbiota, i.e. bacterial communities. However, there is little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent‐producing body surfaces. Here, using high‐throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel (Halobaena caerulea), a seabird with highly developed olfaction that has been suggested to rely on oduor cues during an MHC‐based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with high MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus in which some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical‐producing microbiota in birds.     

Impaired blood-brain barrier in the microbiota-gut-brain axis: Potential role of bipolar susceptibility gene TRANK1

Bipolar disorder (BD) is a common psychiatric illness with high prevalence and disease burden. Accumulating susceptibility genes for BD have been identified in recent years. However, the exact functions of these genes remain largely unknown. Despite its high heritability, gene and environment interaction is commonly accepted as the major contributing factor to BD pathogenesis. Intestine microbiota is increasingly recognized as a critical environmental factor for human health and diseases via the microbiota-gut-brain axis. BD individuals showed altered diversity and compositions in the commensal microbiota. In addition to pro-inflammatory factors, such as interleukin-6 and tumour necrosis factor-α, type 1 interferon signalling pathway is also modulated by specific intestinal bacterial strains. Disruption of the microbiota-gut-brain axis contributes to peripheral and central nervous system inflammation, which accounts for the BD aetiology. Administration of type 1 interferon can induce the expression of TRANK1, which is associated with elevated circulating biomarkers of the impaired blood-brain barrier in BD patients. In this review, we focus on the influence of intestine microbiota on the expression of bipolar gene TRANK1 and propose that intestine microbiota-dependent type 1 interferon signalling is sufficient to induce the over-expression of TRANK1, consequently causing the compromise of BBB integrity and facilitating the entrance of inflammatory mediators into the brain. Activated neuroinflammation eventually contributes to the occurrence and development of BD. This review provides a new perspective on how gut microbiota participate in the pathogenesis of BD. Future studies are needed to validate these assumptions and develop new treatment targets for BD.     

Alterations in the gut microbiota of patients with acquired immune deficiency syndrome

Acquired immune deficiency syndrome (AIDS), caused by infection with human immunodeficiency virus (HIV), is associated with gastrointestinal disease, systemic immune activation and changes in the gut microbiota. Here, we aim to investigate the gut microbiota patterns of HIV‐infected individuals and HIV‐uninfected individuals in populations from South China. We enrolled 33 patients with HIV (14 participants treated with highly active antiretroviral therapy [HAART] for more than 3 months; the remaining 19 individuals had not received treatment) and 35 healthy controls (HC) for a cross‐sectional comparison of gut microbiota using stool samples. Gut microbial communities were profiled by sequencing the bacterial 16S rRNA genes. Dysbiosis was more common among patients with AIDS compared with healthy individuals. Dysbiosis was characterized by decreased α‐diversity, low mean counts of Bacteroidetes, Faecalibacterium, Prevotella, Bacteroides vulgatus, Dialister and Roseburia inulnivorans, and high mean counts of Proteobacteria, Enterococcus, Streptococcus, Lactobacillus, Lachnociostridium, Ruminococcus gnavus and Streptococcus vestibularis. Increased abundance of Bacilli was observed in homosexual patients. Proteobacteria were higher among heterosexual patients with HIV infections. Tenericutes were higher among patients with history of intravenous drug abuse. Restoration of gut microbiota diversity and a significant increase in abundance of Faecalibacterium, Blautia and Bacteroides were found in patients receiving HAART compared to those who did not receive. HIV infection‐associated dysbiosis is characterized by decreased levels of α‐diversity and Bacteroidetes, increased levels of Proteobacteria and the alterations of gut microbiota correlate with the route of HIV transmission. The imbalanced faecal microbiota of HIV infection is partially restored after therapy.     

Analysis of Bacterial and Fungal Communities in Japanese- and Chinese-Fermented Soybean Pastes Using Nested PCR–DGGE

The microbial diversity of Japanese- and Chinese-fermented soybean pastes was investigated using nested PCR–denaturing gradient gel electrophoresis (DGGE). Five Japanese-fermented soybean paste samples and three Chinese-fermented soybean paste samples were analyzed for bacteria and fungi. Extracted DNA was used as a template for PCR to amplify 16S rRNA and 18S rRNA genes. The nearly complete 16S rRNA and 18S rRNA genes were amplified using universal primers, and the resulting products were subsequently used as a template in a nested PCR to obtain suitable fragments for DGGE. Tetragenococcus halophilus and Staphylococcus gallinarum were found to dominate the bacterial microbiota in Japanese samples, whereas Bacillus sp. was detected as the predominant species in Chinese samples. DGGE analysis of fungi in soybean pastes determined the presence of Aspergillus oryzae and Zygosaccharomyces rouxii in most of the Chinese and Japanese samples. Some differences were observed in the bacterial diversity of Japanese- and Chinese-fermented soybean pastes.     

Diversity of gut microbiota increases with aging and starvation in the desert locust

Here we report the effects of starvation and insect age on the diversity of gut microbiota of adult desert locusts, Schistocerca gregaria, using denaturing gradient gel electrophoretic (DGGE) analysis of bacterial 16S rRNA genes. Sequencing of excised DGGE bands revealed the presence of only one potentially novel uncultured member of the Gammaproteobacteria in the guts of fed, starved, young or old locusts. Most of the 16S rRNA gene sequences were closely related to known cultured bacterial species. DGGE profiles suggested that bacterial diversity increased with insect age and did not provide evidence for a characteristic locust gut bacterial community. Starved insects are often more prone to disease, probably because they compromise on immune defence. However, the increased diversity of Gammaproteobacteria in starved locusts shown here may improve defence against enteric threats because of the role of gut bacteria in colonization resistance.     

基于16S rRNA基因序列分析法比较苏尼特双峰驼和阿拉善双峰驼自然发酵酸驼乳的微生物多样性

【目的】传统发酵乳制品是一类未经任何处理自然发酵而成的,其微生态环境未遭破坏,从而乳酸菌的生物学特性和基因多样性得到了很好的保留,具有开发和利用价值。自然发酵酸驼乳常用来治疗多种疾病且效果良好,与其中丰富的乳酸菌资源有着密不可分的联系。然而,目前有关自然发酵酸驼乳微生物菌群及多样性相关研究甚少。因此进一步挖掘内蒙古地区双峰驼自然发酵酸驼乳微生物群落结构和多样性是至关重要的。【方法】本研究采用IlluminaMiseq测序技术,测定了苏尼特和阿拉善双峰驼的自然发酵酸驼乳中微生物16S rRNA V3–V4区序列,并对群落结构和多样性进行了比较分析。【结果】多样性分析表明,苏尼特双峰驼酸驼乳中微生物群落丰富度和种群差异性比阿拉善双峰驼酸驼乳大,细菌多样性也高。在门水平上,苏尼特和阿拉善双峰驼酸驼乳中的菌群均以厚壁菌门(Firmicutes)和变形菌门(Proteobacteria)为主。在属水平上,苏尼特双峰驼酸驼乳主要以乳杆菌属(Lactobacillus)和乳球菌属(Lactococcus)为优势菌群,阿拉善双峰驼酸驼乳以乳杆菌属(Lactobacillus)和醋酸杆菌属(Acetobacter)为优势菌属。此外,肠杆菌属(Enterobacter)、拉乌尔菌属(Raoultella)和明串珠菌属(Leuconostoc)等的含有食源性致病菌和环境污染菌的菌属被检出。综上所述,不同地区不同品种酸驼乳的乳酸菌种类及优势菌群有较大差异,存在显著的地理差异。【结论】通过本研究,不仅对苏尼特和阿拉善双峰驼自然发酵酸驼乳乳酸菌的组成和种类有了明确的认知,为评估发酵酸驼乳微生物群落对消费者身体健康的影响提供了数据基础的同时为今后筛选优势菌群和挖掘新型益生菌奠定基础。     

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards

Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct ‘ecomorphs’ related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk‐crown, trunk‐ground, grass‐bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk‐ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.