Association of aerobic anoxygenic phototrophs and zebra mussels,Dreissena polymorpha,within the littoral zone of Lake Winnipeg

While nutrient loading has affected all levels of Lake Winnipeg’s ecology, its greatest influence has likely been on the microbial community. In addition to eutrophication, zebra mussels (Dreissena polymorpha) have recently invaded the ecosystem and threaten food web dynamics. Their filter-feeding predation and association with bacteria, specifically phototrophs, was investigated. A sampling trip to Lake Winnipeg in October 2017, focused on the isolation, enumeration, and identification of aerobic anoxygenic phototrophs in littoral water, sediment, and tissues of mussels. Gimli, Patricia, and Grand beaches, separated by >15 km across the South Basin, had similar bacterial counts when cultivated on rich organic, BG-11, purple non-sulphur, and K₂TeO₃-supplemented media. Culture-based enumeration on rich organic medium revealed 1.74% of heterotrophs from littoral waters were aerobic anoxygenic phototrophs, and represented 13.98% within sediments. In contrast, 0.48, 1.15, and 0.16% of cultured heterotrophs were aerobic anoxygenic phototrophs within zebra mussel gill, gut, and gonadal tissues, respectively. High-throughput sequencing of bacterial 16S V4 rDNA maintained similar trends in respective bivalve organs, where 0.22, 1.13, and 0.20% of total 16S genes belonged to these phototrophs. Several Sphingomonadaceae isolates were recovered from gut tissues, all with filamentous morphology large enough for predation. Bioaccumulation of metals was also studied in D. polymorpha. All tested associated aerobic anoxygenic phototrophs were capable of resisting the metalloid oxide tellurite. The consistent distribution of aerobic anoxygenic phototrophs within microbial communities across Lake Winnipeg, and their predominance in the gut tissues of zebra mussels suggested bacterial consumption by this invasive species.     

Microbiome of free-living amoebae isolated from drinking water

Free-living amoebae (FLA) are protozoa that can be found in water networks where they prey on bacteria within biofilms. Most bacteria are digested rapidly by phagocytosis, however some are able to survive within amoebae and some are even able to multiply, as it is the case for Legionella pneumophila. These resisting bacteria are a potential health problem as they could also resist to macrophage phagocytosis. Several publications already reported intra-amoebal bacteria but the methods of identification did not allow metagenomic analysis and are partly based on co-culture with one selected amoebal strain. The aim of our study was to conduct a rRNA-targeted metagenomic analysis on amoebae and intra-amoebal bacteria found in drinking water network, to provide the first FLA microbiome in environmental strains. Three sites of a water network were sampled during four months. Culturable FLA were isolated and total DNA was prepared, allowing purification of both amoebal and bacterial DNA. Metagenomic studies were then conducted through 18S or 16S amplicons sequencing. Hartmannella was by far the most represented genus of FLA. Regarding intra-amoebal bacteria, 54 genera were identified, among which 21 were newly described intra-amoebal bacteria, underlying the power of our approach. There were high differences in bacterial diversity between the three sites. Several genera were highly represented and/or found at least in two sites, underlying that these bacteria could be able to multiply within FLA. Our method is therefore useful to identify FLA microbiome and could be applied to other networks to have a more comprehensive view of intra-amoebal diversity.     

Insulin resistance as key factor for linking modulation of gut microbiome to health claims and dietary recommendations to tackle obesity

BackgroundCurrent dietary and public health recommendations addressing obesity do not as yet include recommendations pertaining to the gut microbiome. As a corollary, no microbiome-related health claims made on foods have as yet been proposed.ScopeThe MyNewGut project aims, amongst others, to provide guidance for the establishment of dietary and public health recommendations related to the role microbiome in the onset and development of obesity. Moreover, the project's forthcomings should allow the compilation of a guidance document for microbiome-related health claims.Key findingsOf all the physiological effects resulting from changes in the microbiome, insulin resistance is the most direct diet-modifiable parameter related to obesity. Improving insulin resistance is considered to be the key health benefit conferred by the targeted modulation of the gut microbiome, through the development and application of foods containing microbiome-targeted fibers and micro-organisms.ConclusionsIn order to facilitate guidance for the development of public health and dietary recommendations, as well as for health claim substantiation related to the gut microbiome, foods containing microbiome-targeting dietary fibers and microorganisms will be developed and studies with these foods should provide for the total body of clinical evidence specifically addressing the central theme of ‘insulin resistance’ in obesity, still leaving ample room for the inclusion of other parameters of interest. The latter is pivotal since an impact of other parameters on obesity should be addressed as well, particularly in view of the multifaceted modes of action of the microbiome.     

Stenotrophomonas,Mycobacterium, and Streptomyces in home dust and air: associations with moldiness and other home/family characteristics

Respiratory illnesses have been linked to children's exposures to water‐damaged homes. Therefore, understanding the microbiome in water‐damaged homes is critical to preventing these illnesses. Few studies have quantified bacterial contamination, especially specific species, in water‐damaged homes. We collected air and dust samples in twenty‐one low‐mold homes and twenty‐one high‐mold homes. The concentrations of three bacteria/genera, Stenotrophomonas maltophilia, Streptomyces sp., and Mycobacterium sp., were measured in air and dust samples using quantitative PCR (QPCR). The concentrations of the bacteria measured in the air samples were not associated with any specific home characteristic based on multiple regression models. However, higher concentrations of S. maltophilia in the dust samples were associated with water damage, that is, with higher floor surface moisture and higher concentrations of moisture‐related mold species. The concentrations of Streptomyces and Mycobacterium sp. had similar patterns and may be partially determined by human and animal occupants and outdoor sources of these bacteria.     

Analysis of microbiomes in three traditional starters and volatile components of the Chinese rice wines

Food Science and Biotechnology - To understand the effect of microbial community on the flavor of fermented rice wine, microbiomes in three traditional starters (CMQ, NBQ, and YCQ) from different...     

Insights into evolutionary trends in molecular biology tools in microbial screening for biohydrogen production through dark fermentation

Access to clean energy is vital to combat global warming and climate change, and nothing but hydrogen could better deliver it with ease to secure future energy needs. Biohydrogen could be produced in different routes including photolysis, water-gas shift reaction, dark, photo-fermentation and combination of both. Dark fermentative hydrogen production (DFHP) is efficient in comparison with photo-fermentation and utilizing organic waste ensures land usage and water for agriculture. Several microbes are involved in the process of biohydrogen production via dark fermentation and characterizing them at molecular level unveils holistic approach and understanding. Limited resources were available in terms of molecular tools for microbial characterization and this paper attempts to review the evolution of advanced molecular techniques including their merits and demerits. Understanding the composition of micro-flora is important in DFHP and could be classified as pure, co-cultures, enriched mixed cultures and mixed microbiota. These cultures act as seed sources for batch and continuous fermentations that help in understanding the efficiency of these methods. The schematics and systematic assessment of the various molecular tools (cloning, PCR-DGGE, FISH, NGS, CE-SSCP) for quantification, identification, detection and characterization of the microbial cell activity have been elaborated. Lastly, a comparative tabulation recapitulates the merits and drawbacks of each technique discussed. This provides valued information for choosing the right kind of microbial and molecular assessment tool for future characterization. Such analysis aids in suitable identification and characterization of microflora as potential biocatalysts for biohydrogen production through dark fermentation.     

Role of microbiota function during early life on child's neurodevelopment

BackgroundThere are critical periods during pregnancy and early life when child's neurodevelopment can be altered, where different factors including hormones, stress, genetics, and diet have an important role. Novel studies are indicating that also gut microbiota and maternal obesity can influence child's neurodevelopment.Scope and approachThis review summarises the current concepts related to microbiota-gut-brain axis, including microbiota modulation of the eating behaviour, child's cognitive function and brain structure, microbiota analysis techniques and neurodevelopment assessment in children. Further, we propose and present knowledge about potential mechanisms of action and ways to intervene for disease prevention and treatments, opening up an exciting area with important medical and industrial applications.Key findings and conclusionsThis novel and fast developing research area is indicating that gut microbiota in association with body weight might have an important impact on foetal and child neurodevelopment. However, the exact mechanisms are not known and further research in the field is warranted. Within the MyNewGut Project we aim to analyse the impact of microbiota in association with body weight on cognitive and behaviour development in children. We will study the phylogeny and function of the gut microbial communities in overweight, obese and gestational diabetes pregnancies and in their progeny, in association with infants and children's cognitive and behavioural outcomes. As well, the impact of gut microbiome on brain structure and function during childhood will be evaluated. Results from this study will shed light on the impact of maternal and offspring gut microbiome and body weight on child's neurodevelopment, brain structure and function, and will suggest potential mechanisms for intervention.     

用多元矢量自回归模型推断微生物相互作用关系

识别微生物相互作用关系对理解微生物社团的结构和功能非常重要,一般的推断微生物相互作用关系的计算方法都是基于微生物个体相似性来提出的。比起来自多个不同社区的相互作用网络,一个复杂社区的时间动态性可以揭示更为复杂的相互作用关系。尽管已经提出了很多相似性方法来分析时间序列数据,但是没有有效的多元统计方法来推断和评估作用关系的统计显著性。在本文中,我们提出从人类肠道微生物的时间序列数据来推断出微生物动态相互作用,我们使用多元统计方法——矢量自回归(MVAR)模型,并应用它对重复抗生素扰动的人类肠道微生物时间序列数据集进行网络预测。所涉及的微生物相互作用提供了一个微生物社团的动态观点,这可能是对相似或相关方法的一种新型补充。     

Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data

Method development has always been and will continue to be a core driving force of microbiome science. In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms: ① a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③ a shift from microbiome data analysis to microbiome data science. Some of the recent method-development efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding “Made-in-China” tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.