Gut microbes of mammalian herbivores facilitate intake of plant toxins

The foraging ecology of mammalian herbivores is strongly shaped by plant secondary compounds (PSCs) that defend plants against herbivory. Conventional wisdom holds that gut microbes facilitate the ingestion of toxic plants; however, this notion lacks empirical evidence. We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. Creosote toxins altered the population structure of the gut microbiome to facilitate an increase in abundance of genes that metabolise toxic compounds. In addition, woodrats were unable to consume creosote toxins after the microbiota was disrupted with antibiotics. Last, ingestion of toxins by naïve hosts was increased through microbial transplants from experienced donors. These results demonstrate that microbes can enhance the ability of hosts to consume PSCs and therefore expand the dietary niche breadth of mammalian herbivores.     

Influence of dietary aconitine and nicotine on the gut microbiota of two lepidopteran herbivores

The gut microbiota plays an important role in pheromone production, pesticide degradation, vitamin synthesis, and pathogen prevention in the host animal. Therefore, similar to gut morphology and digestive enzyme activity, the gut microbiota may also get altered under plant defensive compound-induced stress. To test this hypothesis, Dendrolimus superans larvae were fed either aconitine- or nicotine-treated fresh leaves of Larix gmelinii, and Lymantria dispar larvae were fed either aconitine- or nicotine-treated fresh leaves of Salix matsudana. Subsequently, the larvae were sampled 72hr after diet administration and DNA extracted from larval enteric canals were employed for gut microbial 16S ribosomal RNA gene sequencing (338 F and 806 R primers). The sequence analysis revealed that dietary nicotine and aconitine influenced the dominant bacteria in the larval gut and determined their abundance. Moreover, the effect of either aconitine or nicotine on D. superans and L. dispar larvae had a greater dependence on insect species than on secondary plant metabolites. These findings further our understanding of the interaction between herbivores and host plants and the coevolution of plants and insects.     

Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome

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Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris)

Social bees, like honeybees and bumblebees, have a close contact with nest mates of different developmental stages and generations. This could enhance bacterial transfer between nest mates and offers opportunities for direct transfer of symbionts from one generation to the next, resulting in a stable host specific gut microbiota. Gut symbionts of honeybees and bumblebees have been suggested to contribute in digestion and protection against parasites and pathogens. Here we studied the impact of contact with the bumblebee colony on the colonization potential of the bacterial families (i.e., Neisseriaceae, Orbaceae, Lactobacillaceae and Bifidobacteriaceae) occurring in the gut of adult bumblebees (Bombus terrestris). Bacterial profiles of the gut microbiota of B. terrestris were determined based on the hypervariable V4 region of the 16S rRNA using paired‐end Illumina sequencing. In our experiments, we created different groups in which we gradually reduced the contact with nest mates and hive material. We made 3 observations: (i) reducing the contact between the colony and the bumblebee during adult life resulted in a significant drop in the relative abundance of Lactobacillus bombicola and Lactobacillus bombi; (ii) Bifidobacteriaceae required contact with nest mates to colonize the gut of B. terrestris and a significant lower bacterial diversity was observed in bumblebees that were completely excluded from colony contact during the adult life; (iii) Snodgrassella and Gilliamella were able to colonize the gut of the adult bumblebee without any direct contact with nest mates in the adult life stage. These results indicate the impact of the colony life on the diversity of the characteristic bumblebee gut bacteria.     

Evaluation of five antibiotics on larval gut bacterial diversity of Plutella xylostella (Lepidoptera: Plutellidae)

Larvae of the diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae), have rich microbial communities inhabiting the gut, and these bacteria contribute to the fitness of the pest. In this study we evaluated the effects of five antibiotics (rifampicin, ampicillin, tetracycline, streptomycin sulfate and chloramphenicol) on the gut bacterial diversity of P. xylostella larvae. We screened five different concentrations for each antibiotic in a leaf disc assay, and found that rifampicin and streptomycin sulfate at 3 mg/mL significantly reduced the diversity of the bacterial community, and some bacterial species could be rapidly eliminated. The number of gut bacteria in the rifampicin group and streptomycin sulfate group decreased more rapidly than the others. With the increase of antibiotic concentration, the removal efficiency was improved, whereas toxic effects became more apparent. All antibiotics reduced larval growth and development, and eventually caused high mortality, malformation of the prepupae, and hindered pupation and adult emergence. Among the five antibiotics, tetracycline was the most toxic and streptomycin sulfate was a relatively mild one. Some dominant bacteria were not affected by feeding antibiotics alone. Denaturing gradient gel electrophoresis graph showed that the most abundant and diverse bacteria in P. xylostella larval gut appeared in the cabbage feeding group, and diet change and antibiotics intake influenced gut flora abundance. Species diversity was significantly reduced in the artificial diet and antibiotics treatment groups. After feeding on the artificial diet with rifampicin, streptomycin sulfate and their mixture for 10 days, larval gut bacteria could not be completely removed as detected with the agarose gel electrophoresis method.     

常见疾病、抗生素及农药对意大利蜜蜂(Apis mellifera ligustica)肠道微生物多样性的影响研究进展

蜜蜂是对农业生产十分重要的授粉昆虫。蜜蜂肠道微生物与蜜蜂健康有密切关系,但肠道微生物也会受多种外界因素的影响。本文就蜜蜂疾病、抗生素等蜂病治疗药物、农药,以及益生菌的应用等对意大利蜜蜂工蜂肠道微生物影响的研究进行了归纳总结,并对蜜蜂与其肠道菌关系研究进行了展望。     

婴儿肠道双歧杆菌多样性的研究进展

双歧杆菌是婴儿肠道中最丰富的微生物,对婴儿肠道微生物的成熟和稳定有显著影响,与婴儿健康紧密相关。大量研究表明,婴儿肠道中最广泛存在的双歧杆菌有长双歧杆菌、短双歧杆菌和两歧双歧杆菌。母婴之间垂直传递可直接影响婴儿肠道中双歧杆菌各种属的早期定植和相对丰度变化,特别是分娩方式和喂养方式会显著影响婴儿肠道双歧杆菌。此外,胎龄和辅食等因素对婴儿肠道中双歧杆菌的组成与多样性也有一定影响。本文对婴儿肠道双歧杆菌的种属组成、相对丰度变化以及影响其多样性的因素进行了综述,为婴儿双歧杆菌群落的认识提供一定的理论依据。     

Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden

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Gut microbial ecology of lizards: insights into diversity in the wild,effects of captivity,variation across gut regions and transmission

Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in‐depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host‐specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.     

Review: Microbial endocrinology: intersection of microbiology and neurobiology matters to swine health from infection to behavior

From birth to slaughter, pigs are in constant interaction with microorganisms. Exposure of the skin, gastrointestinal and respiratory tracts, and other systems allows microorganisms to affect the developmental trajectory and function of porcine physiology as well as impact behavior. These routes of communication are bi-directional, allowing the swine host to likewise influence microbial survival, function and community composition. Microbial endocrinology is the study of the bi-directional dialogue between host and microbe. Indeed, the landmark discovery of host neuroendocrine systems as hubs of host–microbe communication revealed neurochemicals act as an inter-kingdom evolutionary-based language between microorganism and host. Several such neurochemicals are stress catecholamines, which have been shown to drastically increase host susceptibility to infection and augment virulence of important swine pathogens, including Clostridium perfringens. Catecholamines, the production of which increase in response to stress, reach the epithelium of multiple tissues, including the gastrointestinal tract and lung, where they initiate diverse responses by members of the microbiome as well as transient microorganisms, including pathogens and opportunistic pathogens. Multiple laboratories have confirmed the evolutionary role of microbial endocrinology in infectious disease pathogenesis extending from animals to even plants. More recent investigations have now shown that microbial endocrinology also plays a role in animal behavior through the microbiota–gut–brain axis. As stress and disease are ever-present, intersecting concerns during each stage of swine production, novel strategies utilizing a microbial endocrinology-based approach will likely prove invaluable to the swine industry.     

Community structure of the gut microbiota in sympatric species of wild Drosophila

Many aspects of animal ecology and physiology are influenced by the microbial communities within them. The underlying forces contributing to the assembly and diversity of gut microbiotas include chance events, host‐based selection and interactions among microorganisms within these communities. We surveyed 215 wild individuals from four sympatric species of Drosophila that share a common diet of decaying mushrooms. Their microbiotas consistently contained abundant bacteria that were undetectable or at low abundance in their diet. Despite their deep phylogenetic divergence, all species had similar microbiotas, thus failing to support predictions of the phylosymbiosis hypothesis. Communities within flies were not random assemblages drawn from a common pool; instead, many bacterial operational taxonomic units (OTUs) were overrepresented or underrepresented relative to the neutral expectations, and OTUs exhibited checkerboard distributions among flies. These results suggest that selective factors play an important role in shaping the gut community structure of these flies.     

持续低氧条件下大鼠肠道微生物变化及其与心肌损伤的关联研究

【目的】研究持续性常压低氧对大鼠肠道微生物的影响,并分析其与低氧性心肌肥厚的关联性。【方法】雌性无特异性病原体(specific-pathogen-free, SPF)级SD (Sprague-Dawley)大鼠,按随机数字表法分为2组：常氧组和低氧组。实验开始后,低氧组大鼠置于低氧舱中,氧气浓度设定为10%,持续暴露30 d,常氧组大鼠正常条件饲养。每天记录大鼠体重,并于低氧前(0 d)和低氧后(30 d)分别收集粪便进行16S rRNA基因扩增子测序,测定肠道微生物组的变化。实验结束后进行血常规、血生化和器官指数分析;采用实时定量聚合酶链式反应(quantitativereal-time polymerasechainreaction,qRT-PCR)检测右心室组织中4种分子标志物心房利钠肽基因(atrial natriureticpeptide,ANP)、脑钠肽基因(brainnatriureticpeptide,BNP)、心肌肌球蛋白重链6基因(myosin heavy chain 6, Myh6)、心肌肌球蛋白重链7基因(myosin heavy chain 7, Myh7)...     

Integrated analysis of miRNA and mRNA expression profiles in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis

Insect gut microbiota has been reported to participate in regulating host multiple biological processes including metabolism and reproduction. However, the corresponding molecular mechanisms remain largely unknown. Recent studies suggest that microRNAs (miRNAs) are involved in complex interactions between the gut microbiota and the host. Here, we used next-generation sequencing technology to characterize miRNA and mRNA expression profiles and construct the miRNA–gene regulatory network in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis. A total of 3016 differentially expressed genes (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Based on the integrated analysis of miRNA and mRNA sequencing data, 229 negatively correlated miRNA–gene pairs were identified from the miRNA–mRNA network. Gene ontology enrichment analysis indicated that DEMs could target several genes involved in the metabolic process, oxidation–reduction process, oogenesis, and insulin signaling pathway. Finally, real-time quantitative polymerase chain reaction further verified the accuracy of RNA sequencing results. In conclusion, our study provides the profiles of miRNA and mRNA expressions under antibiotics treatment and provides an insight into the roles of miRNAs and their target genes in the interaction between the gut microbiota and its host.     

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。     

新疆不同栖息地赤麻鸭肠道菌群多样性研究

【目的】探讨天山北麓赤麻鸭肠道细菌多样性及其与栖息地环境之间的关系。【方法】于2017年秋季在天山北麓5个栖息地随机采取新鲜的赤麻鸭粪便,用细菌16S rDNA通用引物扩增V3–V4区并进行高通量测序,使用BLAST、USEARCH和QIIME等软件和在线工具分析各栖息地样品菌群组成与差异。【结果】从赤麻鸭粪便样本中共获得16S rDNA有效序列408 036条,聚类产生1 014个操作分类单元(operational taxonomic unit,OTU)。样品中的细菌分属25个门和397个属。在门分类阶元上,变形菌门和厚壁菌门在所有样品中均为优势菌,相对丰度较高的还包括拟杆菌门、梭杆菌门、放线菌门、蓝藻细菌、螺旋体门、Saccharibacteria和迷踪菌门,但以上细菌在各栖息地样品中的相对丰度存在差异。在属分类阶元上,各栖息地样品的菌群组成差异显著,艾比湖、安集海水库、奎屯水库、蘑菇湖水库和八一水库样品的优势菌分别为鲸杆菌属、巨单胞菌属、假单胞菌属、乳酸菌属和链球菌属。对不同样品菌群组成和差异分析表明,赤麻鸭胃肠道菌群组成受环境和食源的影响较大。【结论】新疆5个栖息地赤麻鸭肠道...     

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high‐throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.     

Combining mutations in HIV-1 protease to understand mechanisms of resistance

HIV-1 develops resistance to protease inhibitors predominantly by selecting mutations in the protease gene. Studies of resistant mutants of HIV-1 protease with single amino acid substitutions have shown a range of independent effects on specificity, inhibition, and stability. Four double mutants, K45I/L90M, K45I/V82S, D30N/V82S, and N88D/L90M were selected for analysis on the basis of observations of increased or decreased stability or enzymatic activity for the respective single mutants. The double mutants were assayed for catalysis, inhibition, and stability. Crystal structures were analyzed for the double mutants at resolutions of 2.2-1.2 A to determine the associated molecular changes. Sequence-dependent changes in protease-inhibitor interactions were observed in the crystal structures. Mutations D30N, K45I, and V82S showed altered interactions with inhibitor residues at P2/P2', P3/P3'/P4/P4', and P1/P1', respectively. One of the conformations of Met90 in K45I/L90M has an unfavorably close contact with the carbonyl oxygen of Asp25, as observed previously in the L90M single mutant. The observed catalytic efficiency and inhibition for the double mutants depended on the specific substrate or inhibitor. In particular, large variation in cleavage of p6(pol)-PR substrate was observed, which is likely to result in defects in the maturation of the protease from the Gag-Pol precursor and hence viral replication. Three of the double mutants showed values for stability that were intermediate between the values observed for the respective single mutants. D30N/V82S mutant showed lower stability than either of the two individual mutations, which is possibly due to concerted changes in the central P2-P2' and S2-S2' sites. The complex effects of combining mutations are discussed.     

椰心叶甲、椰子织蛾肠道菌群多样性分析

[目的] 椰心叶甲、椰子织蛾同属棕榈科食叶性入侵害虫,两者同时取食棕榈科植物却无明显竞争作用,本文通过分子生物学手段对两者的肠道菌群组成、肠道代谢通路进行比对,以此探讨两者食性之间相关性。[方法] 以16S rRNA菌群分析等预测手段对两者肠道微生物群落、代谢通路等进行差异分析。[结果] 椰心叶甲体内变形菌门群落丰度显著高于椰子织蛾,椰子织蛾体内蓝菌门、放线菌门、酸杆菌门、疣微菌门等菌群丰度显著高于椰心叶甲;椰心叶甲体内膦酸酯和亚膦酸盐代谢、N-聚糖合成等肠道代谢通路显著强于椰子织蛾,而椰子织蛾肠道中酮体的合成和降解、维生素B6代谢、核黄素代谢、黄酮和黄酮醇生物合成等代谢通路显著强于椰心叶甲。[结论] 椰子织蛾体内相对较高的酸杆菌门丰度可能导致了其偏好取食纤维素高的椰子老叶,而椰心叶甲则相反。同时,椰子织蛾肠道内显著较高的维生素B含量在其族群发展过程中起到了主要作用。两者细菌丰度以及代谢通路强度的差异可能影响了两者的食性。     

Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis

Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen–microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host’s metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.