Focus: Microbiome: Distinct Ecological Niche of Anal,Oral, and Cervical Mucosal Microbiomes in Adolescent Women

Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes, oral samples with Streptococcus and Prevotella, and cervical samples with Lactobacillus. The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual.     

Anatomy promotes neutral coexistence of strains in the human skin microbiome

1. Download : Download high-res image (201KB)
2. Download : Download full-size image

     

Application of ecological and evolutionary theory to microbiome community dynamics across systems

A fundamental aim of microbiome research is to understand the factors that influence the assembly and stability of host-associated microbiomes, and their impact on host phenotype, ecology and evolution. However, ecological and evolutionary theories applied to predict microbiome community dynamics are largely based on macroorganisms and lack microbiome-centric hypotheses that account for unique features of the microbiome. This special feature sets out to drive advancements in the application of eco-evolutionary theory to microbiome community dynamics through the development of microbiome-specific theoretical and conceptual frameworks across plant, human and non-human animal systems. The feature comprises 11 research and review articles that address: (i) the effects of the microbiome on host phenotype, ecology and evolution; (ii) the application and development of ecological and evolutionary theories to investigate microbiome assembly, diversity and stability across broad taxonomic scales; and (iii) general principles that underlie microbiome diversity and dynamics. This cross-disciplinary synthesis of theoretical, conceptual, methodological and analytical approaches to characterizing host–microbiome ecology and evolution across systems addresses key research gaps in the field of microbiome research and highlights future research priorities.     

The microbiome and childhood diseases: Focus on brain‐gut axis

Many childhood diseases such as autism spectrum disorders, allergic disease, and obesity are on the increase. Although environmental factors are thought to play a role in this increase. The mechanisms at play are unclear but increasing evidence points to an interaction with the gastrointestinal microbiota as being potentially important. Recently this community of bacteria and perturbation of its colonization in early life has been linked to a number of diseases. Many factors are capable of influencing this colonization and ultimately leading to an altered gut microbiota which is known to affect key systems within the body. The impact of the microbial composition of our gastrointestinal tract on systems outside the gut is also becoming apparent. Here we highlight the factors that are capable of impacting on microbiota colonization in early‐life and the developing systems that are affected and finally how this may be involved in the manifestation of childhood diseases. Birth Defects Research (Part C) 105:296–313, 2015. © 2015 Wiley Periodicals, Inc.     

Do Maternal Microbes Shape Newborn Oral Microbes?

Strong evidence suggests that the early composition of the oral microbiota of neonates plays an important role for the postnatal development of the oral health or immune system. However, the relationship between the maternal microbiome and the initial neonatal microbiome remains unclear. In this study, 25 pregnant women and their neonates were recruited, and the samples were collected from the maternal oral cavity, amniotic fluid, placenta and neonatal oral cavity. High-throughput sequencing of 16S rRNA was performed using the Illumina MiSeq platform to analyze the correlation with microbial community structure between the maternal and the neonatal oral cavity. The results indicated that the number of shared OTUs was up to 635 in four groups. The PCoA showed that there were certain similarities in the microbial community structure of the four groups. The dominant bacterial genera of the shared OTUs were consistent with human oral microbes, including Streptococcus, Fusobacterium and Prevotella. The results showed that there might be a correlation between the maternal and neonatal oral microbiome, through the amniotic fluid and placenta.Electronic supplementary materialThe online version of this article (10.1007/s12088-020-00901-7) contains supplementary material, which is available to authorized users.     

Focus: Microbiome: Unraveling the Dynamics of the Human Vaginal Microbiome

Four Lactobacillus species, namely L. crispatus, L. iners, L. gasseri, and L. jensenii, commonly dominate the vaginal communities of most reproductive-age women. It is unclear why these particular species, and not others, are so prevalent. Historically, estrogen-induced glycogen production by the vaginal epithelium has been proffered as being key to supporting the proliferation of vaginal lactobacilli. However, the ‘fly in the ointment’ (that has been largely ignored) is that the species of Lactobacillus commonly found in the human vagina cannot directly metabolize glycogen. It would appear that this riddle has been solved as studies have demonstrated that vaginal lactobacilli can metabolize the products of glycogen depolymerization by α-amylase, and fortunately, amylase activity is found in vaginal secretions. These amylases are presumed to be host-derived, but we suggest that other bacterial populations in vaginal communities could also be sources of amylase in addition to (or instead of) the host. Here we briefly review what is known about human vaginal bacterial communities and discuss how glycogen-derived resources and resource competition might shape the composition and structure of these communities.     

肠道菌群与肿瘤的相关性

人类肠道中有500余种细菌,参与消化、代谢和免疫等生理活动。肠道菌群因其数量庞大、作用显著,被称为人体的"第二基因"。随着研究的不断深入,发现肠道菌群与多种疾病如心脑血管疾病、糖尿病、肥胖、胃肠炎甚至肿瘤的发生息息相关。恶性肿瘤作为一种病死率极高的疾病,近年来与其相关的研究也越来越丰富。研究者们发现,肠道菌群在肺癌、黑色素瘤、消化道肿瘤和血液系统肿瘤等的发生、发展及治疗中发挥着重要的作用,已成为近年来的研究热点。因此,本文对肠道菌群与各类肿瘤的关系研究进展进行综述。     

Gut microbiome and cancer immunotherapy

Gut microbiome has received significant attention for its influences on a variety of host functions, especially immune modulation. With the next-generation sequencing methodologies, more knowledge is gathered about gut microbiome and its irreplaceable role in keeping the balance between human health and diseases is figured out. Immune checkpoint inhibitors (ICIs) are one of the most innovational cancer immunotherapies across cancer types and significantly expand the therapeutic options of cancer patients. However, a proportion of patients show no effective responses or develop immune-related adverse events when responses do occur. More important, it is demonstrated that the therapeutic response or treatment-limiting toxicity of cancer immunotherapy can be ameliorated or diminished by gut microbiome modulation. In this review, we first introduce the relationship between gut microbiome and cancer immunotherapy. And then, we expound the impact of gut microbiome on efficacy and toxicity of cancer immunotherapy. Further, we review approaches to manipulating gut microbiome to regulate response to ICIs. Finally, we discuss the current challenges and propose future directions to improve cancer immunotherapy via gut microbiome manipulation.     

微生物组测序与分析专家共识

在过去的十几年,微生物组相关研究和应用持续升温。微生物组逐渐成为生命科学、环境科学和医学等领域的研究焦点。与此同时,全球多个国家和组织也都积极发起各自的微生物组计划,进行多方面的布局,力争在这一具有广阔前景的领域获得战略地位。此外,无论是科研还是产业应用已经迎来了研究高潮和投融资热潮,微生物组相关产品和服务也不断出现。然而,行业在快速发展的同时,也存在一些不足。由于微生物组测序和分析相关技术和方法发展迅速,各国研究和应用尚未在技术、方案和数据等标准上达成统一,国内行业参与者对微生物组也存在认识不足,对微生物组相关新方法、新技术、新理论等还未能充分掌握和使用。除此之外,已有的一些标准和指南,内容过于简单,实操性也不足,这不仅给科研数据的整合造成了困难和资源浪费,还给相关企业进行不良竞争、以次充好提供了机会。更重要的是,我国尚缺乏微生物组相关的国家标准,国家微生物组计划仍处于筹备过程。在此背景下,中国生物工程学会、中国科学院微生物研究所于2019年6月至2020年3月,共同设立了“微生物组测序与分析专家共识”专项研究课题。中国生物工程学会组织了微生物组相关领域的27位专家以及来自行业内的30多位专业人员,通过分成4个项目小组、召开4轮研讨会后,最终形成了涵盖从微生物采集与保存、DNA提取与建库、高通量基因测序和数据分析以及质控标准品等全流程的“微生物组测序与分析专家共识”。本专家共识具有较强可参考性和可操作性,不仅能指导国内科研和产业机构规范进行微生物组相关产、学、研,还能为国家相关职能部门提供可参考的技术依据,保障规模型和规范化的企业利益,加强行业自律,避免不规范的企业扰乱市场,最终促进微生物组相关产业的良性发展。     

Environmental microbiome engineering for the mitigation of climate change

Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.     

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

1. Download : Download high-res image (231KB)
2. Download : Download full-size image

     

Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens

Clostridium scindens American Type Culture Collection 35704 is capable of converting primary bile acids to toxic secondary bile acids, as well as converting glucocorticoids to androgens by side-chain cleavage. The molecular structure of the side-chain cleavage product of cortisol produced by C. scindens was determined to be 11β-hydroxyandrost-4-ene-3,17-dione (11β-OHA) by high-resolution mass spectrometry, ¹H and ¹³C NMR spectroscopy, and X-ray crystallography. Using RNA-Seq technology, we identified a cortisol-inducible (∼1,000-fold) operon (desABCD) encoding at least one enzyme involved in anaerobic side-chain cleavage. The desC gene was cloned, overexpressed, purified, and found to encode a 20α-hydroxysteroid dehydrogenase (HSDH). This operon also encodes a putative “transketolase” (desAB) hypothesized to have steroid-17,20-desmolase/oxidase activity, and a possible corticosteroid transporter (desD). RNA-Seq data suggests that the two-carbon side chain of glucocorticords may feed into the pentose-phosphate pathway and are used as a carbon source. The 20α-HSDH is hypothesized to function as a metabolic “rheostat” controlling rates of side-chain cleavage. Phylogenetic analysis suggests this operon is rare in nature and the desC gene evolved from a gene encoding threonine dehydrogenase. The physiological effect of 11β-OHAD on the host or other gut microbes is currently unknown.