肠道微生物对肥胖影响

肠道微生物是哺乳动物最密集的微生物群落,也是最多样化的微生物群落之一。随着宏基因组学的不断发展,肠道微生物成为热门的研究领域。肠道微生物具有保护和代谢等功能,在胰岛素抵抗和肥胖等疾病中发挥重要作用。本文介绍了肠道微生物及其代谢物通过调节食欲、神经递质合成分泌、炎性反应进而调节肥胖,探讨了肠道微生物的影响因素,展望了肠道微生物对治疗人类肥胖的应用前景。     

The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis

The gut microorganisms in some animals are reported to include a core microbiota of consistently associated bacteria that is ecologically distinctive and may have coevolved with the host. The core microbiota is promoted by positive interactions among bacteria, favoring shared persistence; its retention over evolutionary timescales is evident as congruence between host phylogeny and bacterial community composition. This study applied multiple analyses to investigate variation in the composition of gut microbiota in drosophilid flies. First, the prevalence of five previously described gut bacteria (Acetobacter and Lactobacillus species) in individual flies of 21 strains (10 Drosophila species) were determined. Most bacteria were not present in all individuals of most strains, and bacterial species pairs co-occurred in individual flies less frequently than predicted by chance, contrary to expectations of a core microbiota. A complementary pyrosequencing analysis of 16S rRNA gene amplicons from the gut microbiota of 11 Drosophila species identified 209 bacterial operational taxonomic units (OTUs), with near-saturating sampling of sequences, but none of the OTUs was common to all host species. Furthermore, in both of two independent sets of Drosophila species, the gut bacterial community composition was not congruent with host phylogeny. The final analysis identified no common OTUs across three wild and four laboratory samples of D. melanogaster. Our results yielded no consistent evidence for a core microbiota in Drosophila. We conclude that the taxonomic composition of gut microbiota varies widely within and among Drosophila populations and species. This is reminiscent of the patterns of bacterial composition in guts of some other animals, including humans.     

Consumption of dietary sugar by gut bacteria determines Drosophila lipid content

Gut microorganisms are essential for the nutritional health of many animals, but the underlying mechanisms are poorly understood. This study investigated how lipid accumulation by adult Drosophila melanogaster is reduced in flies associated with the bacterium Acetobacter tropicalis which displays oral–faecal cycling between the gut and food. We demonstrate that the lower lipid content of A. tropicalis-colonized flies relative to bacteria-free flies is linked with a parallel bacterial-mediated reduction in food glucose content; and can be accounted for quantitatively by the amount of glucose acquired by the flies, as determined from the feeding rate and assimilation efficiency of bacteria-free and A. tropicalis-colonized flies. We recommend that nutritional studies on Drosophila include empirical quantification of food nutrient content, to account for likely microbial-mediated effects on diet composition. More broadly, this study demonstrates that selective consumption of dietary constituents by microorganisms can alter the nutritional balance of food and, thereby, influence the nutritional status of the animal host.     

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.     

Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)

Bacterial gut symbiont communities are critical for the health of many insect species. However, little is known about how microbial communities vary among host species or how they respond to anthropogenic disturbances. Bacterial communities that differ in richness or composition may vary in their ability to provide nutrients or defenses. We used deep sequencing to investigate gut microbiota of three species in the genus Bombus (bumble bees). Bombus are among the most economically and ecologically important non-managed pollinators. Some species have experienced dramatic declines, probably due to pathogens and land-use change. We examined variation within and across bee species and between semi-natural and conventional agricultural habitats. We categorized as ‘core bacteria'' any operational taxonomic units (OTUs) with closest hits to sequences previously found exclusively or primarily in the guts of honey bees and bumble bees (genera Apis and Bombus). Microbial community composition differed among bee species. Richness, defined as number of bacterial OTUs, was highest for B. bimaculatus and B. impatiens. For B. bimaculatus, this was due to high richness of non-core bacteria. We found little effect of habitat on microbial communities. Richness of non-core bacteria was negatively associated with bacterial abundance in individual bees, possibly due to deeper sampling of non-core bacteria in bees with low populations of core bacteria. Infection by the gut parasite Crithidia was negatively associated with abundance of the core bacterium Gilliamella and positively associated with richness of non-core bacteria. Our results indicate that Bombus species have distinctive gut communities, and community-level variation is associated with pathogen infection.     

The infant gut resistome associates with E. coli,environmental exposures,gut microbiome maturity,and asthma-associated bacterial composition

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Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome

Metagenomics is a powerful tool that allows for the culture-independent analysis of complex microbial communities. One of the most complex and dense microbial ecosystems known is that of the human distal colon, with cell densities reaching up to 10¹² per gram of faeces. With the majority of species as yet uncultured, there are an enormous number of novel genes awaiting discovery. In the current study, we conducted a functional screen of a metagenomic library of the human gut microbiota for potential salt-tolerant clones. Using transposon mutagenesis, three genes were identified from a single clone exhibiting high levels of identity to a species from the genus Collinsella (closest relative being Collinsella aerofaciens) (COLAER_01955, COLAER_01957 and COLAER_01981), a high G+C, Gram-positive member of the Actinobacteria commonly found in the human gut. The encoded proteins exhibit a strong similarity to GalE, MurB and MazG. Furthermore, pyrosequencing and bioinformatic analysis of two additional fosmid clones revealed the presence of an additional galE and mazG gene, with the highest level of genetic identity to Akkermansia muciniphila and Eggerthella sp. YY7918, respectively. Cloning and heterologous expression of the genes in the osmosensitive strain, Escherichia coli MKH13, resulted in increased salt tolerance of the transformed cells. It is hoped that the identification of atypical salt tolerance genes will help to further elucidate novel salt tolerance mechanisms, and will assist our increased understanding how resident bacteria cope with the osmolarity of the gastrointestinal tract.     

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.     

Classification and quantification of bacteriophage taxa in human gut metagenomes

Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, ‘Group 936 lactococcal phages'' are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage–host network of the human gut was established and includes numerous novel host–phage associations.     

人体肠道4 644株代表菌次级代谢产物生物合成基因簇挖掘与耐药及毒力基因分析

为了更好地从肠道微生物组中挖掘新的次级代谢产物、了解肠道微生物组编码的抗生素耐药基因和毒力因子情况,本研究基于4 644株人体肠道微生物代表菌的基因组序列,对其编码的次级代谢产物基因簇、抗生素耐药基因和毒力因子进行了预测分析。经antiSMASH预测分析发现,超过60%的代表菌编码至少1个次级代谢产物基因簇,并从8个未可培养菌中发现了8个潜在的新颖次级代谢产物基因簇。人体肠道中的次级代谢产物主要由梭菌纲（Clostridia）、芽孢杆菌纲（Bacilli）、γ-变形菌纲（Gammaproteobacteria）、拟杆菌纲（Bacteroidia）、放线菌纲（Actinobacteria）和厚壁菌纲（Negativicutes）6类细菌编码的非核糖体多肽合成酶（nonribosomal peptide synthetase,NRPS）、细菌素、芳基多烯类化合物、萜烯、β-丙内酯、NRPS-样蛋白组成。经PathoFact预测分析发现,抗生素耐药基因和毒力因子在代表性菌株中分布广泛,但潜在病原菌编码频率更高。潜在病原菌中编码外膜蛋白、PapC N-端结构域、PapC C-端结构域、肽酶M16失活结构域等分泌型毒素和硝基还原酶家族、AcrB/AcrD/AcrF家族、PLD-样结构域、Cupin结构域、假定溶血素、S24-样肽酶、磷酸转移酶家族、内切核酸酶/外切核酸酶/磷酸酶家族、乙二醛酶/博莱霉素抗性等非分泌型毒素的频率较高。该研究将为进一步从肠道微生物组中挖掘新的微生物天然产物、了解肠道微生物的定殖与感染机制,为肠道微生物相关疾病提供靶向防治策略等奠定基础。     

肠道微生物功能宏基因组学与代谢组学关联分析方法研究进展

近年来基于高通量基因测序的微生物组学研究极大加深了人们对微生物与健康和疾病关系的认识。然而基因测序方法不能直接测定微生物的功能活性,难以鉴定微生物中的关键功能分子,单独使用无法回答肠道微生物何种成员通过何种方式影响宿主等关键科学问题。单一组学研究弊端尽显,多组学联用势在必行。肠道微生物代谢组学以微生物群落所有小分子代谢物为研究对象,可发现肠道微生物随宿主病理生理变化的关键代谢物,为微生物组-宿主互作机制研究提供线索,成为微生物组学研究的重要补充。肠道微生物功能基因组学与代谢组学关联分析在宿主生理、疾病病理、药物药理等方面取得众多进展,展现良好应用前景。然而目前肠道微生物功能基因组学与代谢组学关联分析存在方法滥用、相关性结论与生物学知识相悖等突出问题。为帮助正确应用肠道微生物功能宏基因组学与代谢组学关联分析,本文综述了各种多组学数据整合分析方法的原理、优缺点与适用范围,并给出了应用建议。     

Massive expansion of human gut bacteriophage diversity

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The Human Intestinal Microbiome: A New Frontier of Human Biology

To analyze the vast number and variety of microorganisms inhabitingthe human intestine, emerging metagenomic technologies are extremelypowerful. The intestinal microbes are taxonomically complexand constitute an ecologically dynamic community (microbiota)that has long been believed to possess a strong impact on humanphysiology. Furthermore, they are heavily involved in the maturationand proliferation of human intestinal cells, helping to maintaintheir homeostasis and can be causative of various diseases,such as inflammatory bowel disease and obesity. A simplifiedanimal model system has provided the mechanistic basis for themolecular interactions that occur at the interface between suchmicrobes and host intestinal epithelia. Through metagenomicanalysis, it is now possible to comprehensively explore thegenetic nature of the intestinal microbiome, the mutually interactingsystem comprising the host cells and the residing microbialcommunity. The human microbiome project was recently launchedas an international collaborative research effort to furtherpromote this newly developing field and to pave the way to anew frontier of human biology, which will provide new strategiesfor the maintenance of human health.     

Intrinsic resistance to aminoglycosides in Enterococcus faecium is conferred by the 16S rRNA m5C1404-specific methyltransferase EfmM

Aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. Here we show that aminoglycoside resistance in Enterococcus faecium strain CIP 54-32 is conferred by the chromosomal gene efmM, encoding the E. faecium methyltransferase, as well as by the previously characterized aac(6′)-Ii that encodes a 6′-N-aminoglycoside acetyltransferase. Inactivation of efmM in E. faecium increases susceptibility to the aminoglycosides kanamycin and tobramycin, and, conversely, expression of a recombinant version of efmM in Escherichia coli confers resistance to these drugs. The EfmM protein shows significant sequence similarity to E. coli RsmF (previously called YebU), which is a 5-methylcytidine (m⁵C) methyltransferase modifying 16S rRNA nucleotide C1407. The target for EfmM is shown by mass spectrometry to be a neighboring 16S rRNA nucleotide at C1404. EfmM uses the methyl group donor S-adenosyl-L-methionine to catalyze formation of m⁵C1404 on the 30S ribosomal subunit, whereas naked 16S rRNA and the 70S ribosome are not substrates. Addition of the 5-methyl to C1404 sterically hinders aminoglycoside binding. Crystallographic structure determination of EfmM at 2.28 Å resolution reveals an N-terminal domain connected to a central methyltransferase domain that is linked by a flexible lysine-rich region to two C-terminal subdomains. Mutagenesis of the methyltransferase domain established that two cysteines at specific tertiary locations are required for catalysis. The tertiary structure of EfmM is highly similar to that of RsmF, consistent with m⁵C formation at adjacent sites on the 30S subunit, while distinctive structural features account for the enzymes'' respective specificities for nucleotides C1404 and C1407.     

环境耐药组及其健康风险的宏基因组学研究策略和方法

抗生素耐药性在环境中的发展和传播对人体健康造成潜在风险。随着高通量测序技术和生物信息学方法的不断发展,宏基因组学技术被广泛应用于不同环境样本的抗生素耐药组研究。本文介绍了两种针对环境耐药组筛查的宏基因组学分析方法,总结了当前主流的生物信息学软件和数据库,并阐述了环境耐药组的风险评估框架和基于宏基因组学技术的相关实践,以期为环境耐药组的监测、风险评估和管控提供可行的路线图。