Phages to shape the gut microbiota?

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Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota

Changes in the gut microbiota during pathogen infection are often predicted to influence disease outcomes. However, studies exploring whether pathogens induce microbiota shifts have yielded inconsistent results. This suggests that variation in infection, rather than the presence of infection alone, might shape pathogen–microbiota relationships. For example, most hosts are coinfected with multiple pathogens simultaneously, and hosts vary in how long they are infected, which may amplify or diminish microbial shifts expected in response to a focal pathogen. We used a longitudinal anthelmintic treatment study of free-ranging African buffalo (Syncerus caffer) to examine whether (i) coinfection with bovine tuberculosis (Mycobacterium bovis, TB) and gastrointestinal nematodes, and (ii) the duration of TB infection, modified effects of single pathogens on the gut microbiota. By accounting for the interaction between TB and nematodes, we found that coinfection affected changes in microbial abundance associated with single infections. Furthermore, the duration of TB infection predicted more microbiota variation than the presence of TB. Importantly, coinfection and infection duration had nearly as much influence on microbial patterns as demographic and environmental factors commonly examined in microbiota research. These findings demonstrate that acknowledging infection heterogeneities may be crucial to understanding relationships between pathogens and the gut microbiota.Subject terms: Microbiome, Infectious diseases     

Modelling the effect of birth and feeding modes on the development of human gut microbiota

The human gut microbiota is transmitted from mother to infant through vaginal birth and breastfeeding. Bifidobacterium, a genus that dominates the infants’ gut, is adapted to breast milk in its ability to metabolize human milk oligosaccharides; it is regarded as a mutualist owing to its involvement in the development of the immune system. The composition of microbiota, including the abundance of Bifidobacteria, is highly variable between individuals and some microbial profiles are associated with diseases. However, whether and how birth and feeding practices contribute to such variation remains unclear. To understand how early events affect the establishment of microbiota, we develop a mathematical model of two types of Bifidobacteria and a generic compartment of commensal competitors. We show how early events affect competition between mutualists and commensals and microbe-host-immune interactions to cause long-term alterations in gut microbial profiles. Bifidobacteria associated with breast milk can trigger immune responses with lasting effects on the microbial community structure. Our model shows that, in response to a change in birth environment, competition alone can produce two distinct microbial profiles post-weaning. Adding immune regulation to our competition model allows for variations in microbial profiles in response to different feeding practices. This analysis highlights the importance of microbe–microbe and microbe–host interactions in shaping the gut populations following different birth and feeding modes.     

Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals

The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.     

取食聚苯乙烯塑料对黄粉虫幼虫肠道微生物群落的影响北大核心

随着塑料在人类社会中的普及,越来越多的废弃塑料及其前体物质被遗留在环境中,且其在自然环境中的降解速度十分缓慢,为此寻找有效的降解途径成为亟待解决的科学问题。【目的】探究利用黄粉虫(Tenebrio molitor)幼虫取食聚苯乙烯对其肠道微生物种群及其代谢路径的响应,以期通过食物诱导寻找一条生物降解和利用聚苯乙烯的有效途径。【方法】以聚苯乙烯为唯一食物来源喂饲黄粉虫幼虫,通过测量幼虫存活率和个体的体重来测定其生长发育情况;通过对其肠道内容物进行16S rRNA基因测序,分析其肠道菌群结构的变化;采用京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)分析法来预测相关功能基因。【结果】取食聚苯乙烯黄粉虫幼虫存活率和体重均下降,聚苯乙烯塑料明显减少;取食聚苯乙烯的黄粉虫幼虫肠道菌群丰度与多样性明显减少,在门水平,取食聚苯乙烯的黄粉虫幼虫肠道的优势菌为变形菌门(Proteobacteria)、软壁菌门(Tenericutes)和厚壁菌门(Firmicutes);在属水平,取食聚苯乙烯的黄粉虫幼虫肠道优势菌为螺旋体菌属(Spiroplasma)、肠杆菌(Enterobacillus)和大肠埃氏-志贺氏菌(Escherichia-Shigella);通过KEGG功能预测,找到与芳香类和烷烃降解功能相关的基因共18种,取食聚苯乙烯组黄粉虫幼虫肠道菌群降解聚苯乙烯相关通路丰度升高,相关基因表达增强。【结论】聚苯乙烯可以为黄粉虫幼虫生长发育提供一定的物质和能量,且能够使其完成一个世代过程;幼虫长时间取食单一食物后,其肠道菌群结构会发生目标性变化,利用KEGG预测能够找到与聚苯乙烯代谢相关的基因,为后续研究工作提供了有价值的依据。     

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.     

Feeding Jerusalem artichoke reduced skatole level and changed intestinal microbiota in the gut of entire male pigs

Different levels of dried Jerusalem artichoke were fed to entire male pigs 1 week before slaughter. The objective was to investigate the effect on skatole level in the hindgut and in adipose tissue, as well as the effect on microflora and short-chain fatty acids (SCFA) in the hindgut. Five experimental groups (n = 11) were given different dietary treatments 7 days before slaughtering: negative control (basal diet), positive control (basal diet + 9% chicory-inulin), basal diet + 4.1% Jerusalem artichoke, basal diet + 8.1% Jerusalem artichoke and basal diet + 12.2% Jerusalem artichoke. Samples from colon, rectum, faeces and adipose tissue were collected. Effect of dietary treatment on skatole, indole and androstenone levels in adipose tissue and on skatole, indole, pH, dry matter (DM), microbiota and SCFA in the hindgut was evaluated. Feeding increasing levels of Jerusalem artichoke to entire male pigs reduced skatole in digesta from colon and in faeces (linear, P < 0.01). There was also a tendency towards a decreased level of skatole in adipose tissue (linear, P = 0.06). Feeding Jerusalem artichoke decreased DM content in colon and faeces and pH in colon (linear, P < 0.01). Increasing levels of Jerusalem artichoke resulted in a reduced level of Clostridium perfringens in both colon and rectum (linear, P < 0.05) and a tendency towards decreased levels of enterobacteria in colon (linear, P = 0.05). Further, there was an increase in total amount of SCFA (linear, P < 0.05), acetic acid (linear, P < 0.05) and valerianic acid (linear, P < 0.01) in faeces. In conclusion, adding dried Jerusalem artichoke to diets for entire male pigs 1 week before slaughter resulted in a dose-dependent decrease in skatole levels in the hindgut and adipose tissue. The reduced skatole levels might be related to the decrease in C. perfringens and the increase in SCFA with subsequent reduction in pH.     

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

To explain differences in gut microbial communities we must determine how processes regulating microbial community assembly (colonization, persistence) differ among hosts and affect microbiota composition. We surveyed the gut microbiota of threespine stickleback (Gasterosteus aculeatus) from 10 geographically clustered populations and sequenced environmental samples to track potential colonizing microbes and quantify the effects of host environment and genotype. Gut microbiota composition and diversity varied among populations. These among-population differences were associated with multiple covarying ecological variables: habitat type (lake, stream, estuary), lake geomorphology and food- (but not water-) associated microbiota. Fish genotype also covaried with gut microbiota composition; more genetically divergent populations exhibited more divergent gut microbiota. Our results suggest that population level differences in stickleback gut microbiota may depend more on internal sorting processes (host genotype) than on colonization processes (transient environmental effects).     

强化玉米饮食对小鼠肠道菌群结构和功能的影响

【目的】采用高通量测序方法研究强化玉米饮食对小鼠肠道菌群结构的影响以及可提高宿主糖代谢相关菌群功能基因的分析。【方法】分别给予两组小鼠(各10只)常规饮食和强化玉米饮食(1/4的玉米粉加3/4的常规饮食成分),喂养10周,之后采集小鼠粪便样本,提取DNA,使用高通量测序仪进行宏基因组测序分析,比较两组小鼠肠道菌群和功能基因的差异。【结果】两组小鼠的终末体重没有明显差异。各样本DNA的测序有效率足够,肠道菌群的多样性存在一定差异。属放线菌门(Actinobacteria)的双歧杆菌(Bifidobacteriales)-B.pseudolongum分支和Coriobacteriia-Collinsella/Enterorhabdus分支的丰度在强化玉米饮食组的小鼠中显著升高,相应的宏基因组中涉及糖酵解和胆汁酸合成的一些酶和功能单元的含量也在强化玉米饮食组显著升高。【结论】强化玉米饮食可以提高肠道菌群中双歧杆菌等益生菌的丰度,增加宏基因组糖脂代谢相关基因和通路的含量,从而可能促进宿主的糖代谢功能。     

造血干细胞移植术对肠道菌群结构的影响

目的监测造血干细胞移植术（Hematopoietic stem cell transplantation,HSCT）前后肠道菌群结构的动态变化。方法收集3例造血干细胞移植患者手术前后8个时间点的粪便样品,提取样品总DNA进行16S rRNA基因的V3区的bar coded 454焦磷酸测序,并用MANOVA、聚类分析、Pearson相关等统计方法对菌群结构的变化进行动态分析。结果 HSCT移植前,经过放、化疗及预防性抗生素治疗,患者的肠道菌群结构和组成发生显著的改变,多样性明显减少;移植4周后,菌群多样性有恢复的趋势,但菌群结构和组成与治疗前仍有明显的差异。整个HSCT过程中,Escherichia/Shigella及Enterococcus属变成肠道中最优势的细菌类群。结论肠道菌群结构在HSCT术前已发生显著的改变,机会致病菌Escherichia/Shigella及Enterococcus属成为HSCT患者肠道中最优势的细菌类群。     

Seasonal variation in structure and function of gut microbiota in Pomacea canaliculata

Gut microbiota is associated with host health and its environmental adaption, influenced by seasonal variation. Pomacea canaliculata is one of the world''s 100 worst invasive alien species. Here, we used high‐throughput sequencing of the 16S rRNA gene to analyze the seasonal variation of gut microbiota of P. canaliculata. The results suggested that the predominant gut microbial phyla of P. canaliculata included Firmicutes and Proteobacteria, which helped digest plant food and accumulate energy. The gut microbiota of P. canaliculata in summer group showed the highest diversity, whereas the winter group possessed the lowest, probably due to the shortage of food resources of P. canaliculata in winter. Principal coordinate analysis analysis based on unweighted unifrac and weighted unifrac indicated that the composition of gut microbiota of P. canaliculata significantly varied across seasons. Bacteroidetes tended to be enriched in summer by linear discriminant analysis effect size analysis. Actinobacteria and Cyanobacteria were extremely abundant in autumn, while Fusobacteria and Cetobacterium enriched in winter. In conclusion, the structure of the gut microbiota of P. canaliculata was significantly different among seasons, which was beneficial to the environment adaptation and the digestion and metabolism of food during different periods.     

Beneficial modulation of the gut microbiota

The human gut microbiota comprises approximately 100 trillion microbial cells and has a significant effect on many aspects of human physiology including metabolism, nutrient absorption and immune function. Disruption of this population has been implicated in many conditions and diseases, including examples such as obesity, inflammatory bowel disease and colorectal cancer that are highlighted in this review. A logical extension of these observations suggests that the manipulation of the gut microbiota can be employed to prevent or treat these conditions. Thus, here we highlight a variety of options, including the use of changes in diet (including the use of prebiotics), antimicrobial-based intervention, probiotics and faecal microbiota transplantation, and discuss their relative merits with respect to modulating the intestinal community in a beneficial way.     

Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals

The gut microbiota of mammals underpins the metabolic capacity and health of the host. Our understanding of what influences the composition of this community has been limited primarily to evidence from captive and terrestrial mammals. Therefore, the gut microbiota of southern elephant seals, Mirounga leonina, and leopard seals, Hydrurga leptonyx, inhabiting Antarctica were compared with captive leopard seals. Each seal exhibited a gut microbiota dominated by four phyla: Firmicutes (41.5 ± 4.0%), Fusobacteria (25.6 ± 3.9%), Proteobacteria (17.0 ± 3.2%) and Bacteroidetes (14.1 ± 1.7%). Species, age, sex and captivity were strong drivers of the composition of the gut microbiota, which can be attributed to differences in diet, gut length and physiology and social interactions. Differences in particular prey items consumed by seal species could contribute to the observed differences in the gut microbiota. The longer gut of the southern elephant seal provides a habitat reduced in available oxygen and more suitable to members of the phyla Bacteroidetes compared with other hosts. Among wild seals, 16 ‘core’ bacterial community members were present in the gut of at least 50% of individuals. As identified between southern elephant seal mother–pup pairs, ‘core’ members are passed on via vertical transmission from a young age and persist through to adulthood. Our study suggests that these hosts have co‐evolved with their gut microbiota and core members may provide some benefit to the host, such as developing the immune system. Further evidence of their strong evolutionary history is provided with the presence of 18 shared ‘core’ members in the gut microbiota of related seals living in the Arctic. The influence of diet and other factors, particularly in captivity, influences the composition of the community considerably. This study suggests that the gut microbiota has co‐evolved with wild mammals as is evident in the shared presence of ‘core’ members.     

肠道微生物与骨质疏松相关性的研究进展

随着人口老龄化问题的加剧,骨质疏松症的高发生率降低了人们的生活质量。越来越多的证据表明,肠道微生物群与骨代谢联系密切,肠道微生物群稳态的破坏会导致宿主的病理生理反应,从而引起骨质疏松。通过研究两者之间的相互作用,或许能为骨质疏松症的预防及相关诊疗提供有价值的帮助。本文就目前肠道微生物与骨质疏松症相关机制和主要治疗的研究现状作一综述。     

Lessons from the diet: Captivity and sex shape the gut microbiota in an oviparous lizard (Calotes versicolor)

Studies have indicated that the abundance and community structure of gut microbiota are altered by diet. In this study, next‐generation sequencing of the 16S rRNA gene amplicon was performed to evaluate variations in the gut microbiota of wild and captive individuals of both sexes of Calotes versicolor. The results showed that there was a significant sex difference in microbial community structure for wild C. versicolor, Bacteroide was the dominant genus in wild females (WF), whereas Ochrobactrum was the dominant genus in wild males (WM). Acinetobacter and Hymenobacter were the dominant genera in WF, while Clostridium was the dominant genus in captive females (CF). The results indicated that differences in diet between wild and captive C. versicolor also resulted in variations in gut microbiota. Thus, it was not surprising that captivity and sex shape the gut microbiota in C. versicolor. In summary, the fundamental information presented about the gut microbiota of both sexes of wild (and captive females) C. versicolor, indicates that the artificial environments are not suitable for the wild C. versicolor.