Abstract:The human microbiota is the ecological community of commensal, the aggregate of symbiotic and pathogenic microorganisms that resides on or within any of several human tissues and biofluids. Human microbiota can be considered as a new ‘organ’ due to its important role in maintaining good health. The interaction mechanisms between microbe and host are comprehensive and complex. The dysbiosis of human microbiota is closely related to the process from diseases occurrence to development. Here we outlined the importance of microbiota study and reviewed the current researches worldwide on the links among disease, health and human microbiota.

Abstract:Oral diseases affect over half of world’s population and cost the health care the same budget as for the top ten mortality diseases. Moreover, oral infections are associated with systemic or chronic diseases such as preterm birth, atherosclerosis, cirrhosis, diabetes and Alzheimer’s disease. Hence, oral microbiome has always been one of the major targets of Human Microbiome Projects. Compared to other body sites, oral microbiome research is characterized by easily-accessible sampling, convenience in phenotyping host responses and directness and high efficacy of intervention approaches. In addition, over 65% of oral bacteria groups are deemed culturable, and genomes of representative strains from these groups have mostly been sequenced. Therefore, oral microbiome is becoming an exceptional research model and basis of technological demonstration for the fundamental questions of human microbiome research, such as inter-species interaction networks, impact of local infection on remote organs, and predictive modeling of chronic diseases, etc. By reviewing the recent scientific and technological progresses in oral microbiome study, here we advocate for the initiation of China Human Oral Microbiome Project (CHOMP), which calls for the collaborative and synergistic efforts from academic, clinical and industrial fronts for exploring and developing strategies and solutions for personalized prognosis, diagnosis and therapy for oral and systemic diseases based on oral microbiome.

Abstract:Human Microbiome Project has been initiated for 10 years. Many studies revealed the crucial roles of human microbiome in human health and diseases. Human virome including human viruses and bacterial phages is a key component of human microbiome and can be associated with human health. Here, by reviewing the latest research progresses in human gut virome studies, we show the features of human gut virome, interactions between human virome, bacteriome and human cells, impacts on human health, as well as strategies and challenges in human gut virome study. We further explore the feasibility in using human gut virome for medical applications.

Abstract:Caves are subsurface spaces and tunnels formed by the dissolution of rocks or during the cooling process of lava. Caves spread all over the world, containing a large amount of microbial resources. Being dark and humid, with relatively stable temperature and poor nutrition, and as a kind of extreme ecosystem, caves maintain highly specialized microbiomes. Study of cave microbial communities revealed its structure and function, facilitated the understanding of geographic distribution of cave microbiomes, deepened the understanding of subterranean ecosystems, and provided guidance for cave painting protection and microbial outbreak inhibition. This paper summarizes research techniques and progresses of cave microbiomes, as well as the characteristic chemoautotrophic microbiomes in caves.

Abstract:[Objective] This study was aimed to study the difference in respiration, bacterial diversity and community composition of permafrost layer and active layer, and methane consumption potential, and to find the active methylotrophs in soil that has high methane consumption potential. [Methods] Soils were sampled from Adventdalen (Svalbard), Ny-Alesund (Svalbard), Kurungnakh Third terrace (Lena delta) and Lena delta First terrace (Lena delta), including active layers and their corresponding permafrost layers, coming from one intact core at each site in 2013 and they were incubated at 10 ℃ in darkness for 26 days, with or without isotope 13-C labeled methane. Miseq sequencing and quantitative PCR of 16S ribosomal RNA gene and particulate methane monooxygenase pmoA gene were performed to assess difference of bacterial abundance, bacterial diversity and community composition of permafrost layer and active layer. Stable isotope probing experiment with 13-C labeled methane as carbon source was performed to reveal the active methanotrophs in geographically distinct arctic soils. [Results] Active layer soil had higher respiration rate than its permafrost soil, which was positively correlated with the difference of bacterial communities. The respiration rate of active layer ranged from 61 to 623 nmol CO₂/(g dws·d), while exceptionally high respiration rate of 7293/(g dws·d) was observed in LF active layer, and the respiration rate of permafrost layer varied from 47 to 523 nmol CO₂/(g dws·d). The average respiration of Lena delta was 17 times higher than that of Svalbard. Accordingly, active layer had higher bacterial diversity and higher abundance than permafrost soil where the relative abundance of 10 families in active layer were significantly higher than its permafrost. These bacterial families were mainly affiliated with Proteobacteria and Acidobacteria, such as Hyphomicrobiaceae, Solibacteraceae, Sinobacteraceae and their relative abundance was between from 4.3% to 18.6%, 2.6 and 23.7 times higher than that in permafrost layer soil. In Lena delta First terrace active layer with extremely high respiration rate, 6 families (mainly Bacteroidales and Gracilibacteraceae) were found with significant higher relative abundance (26.9%) than in other soils. Only active layer soil from Kurungnakh was observed to have strong methane oxidation potential. The methane oxidation rate in Kurungnakh active layer soil was 55.9 nmol CH₄/(g dws·d). And dominant active methylotrophs of Kurungnakh active layer were phylogenetically affiliated with Crenothrix and type I methane oxidizers (Methylobacterium). [Conclusion] The respiration rate of active layer was higher than its permafrost and with high heterogeneity and this could be well explained by difference of bacterial community composition and bacterial abundance in permafrost and active layer. Repeated thawing and refreezing of active layer has developed characteristic community structure that are key drivers for the turnover of the carbon pool, mainly including Hyphomicrobiaceae, Solibacteraceae and Sinobacteraceae. All these results suggest that microbial community structure in permafrost would go through a succession with a direction to that in its active layer, which might play important role in fixed carbon transformation in permafrost. These results provide a mechanistic understanding towards better optimization of soil carbon emission model under global change scenarios.

Abstract:[Objective] This study aimed to identify the key bacteria during the microbial degradation of pyrene in the sediments from Bohai sea and the potential interactions among these bacteria. [Methods] We set up the microcosms system with pyrene as the sole carbon source, apllied the Illumina Hiseq 2500 to reveal the bacterial communities, and then predicted the bacterial ecological interactions using CCLasso algorithm. [Results] The concentration of pyrene decreased by (67.07±2.37)% after 30 days and meanwhile the structures of bacterial communities were distinctly changed. The significantly enriched population consisted of Alphaproteobacteria, Flavobacteriia and Planctomycetia, whereas the relative abundances of Deltaproteobacteria, Anaerolineae and Spirochaetes decreased. The microbial ecological network was constructed and composed of 29 nodes and 143 edges. The classified genera with relatively high degree values included Erythrobacter and Planctomyces. The strong associations were observed between the genus Erythrobacter and some unclassified genera affiliated to the family Flavobacteriaceae and the class Alphaproteobacteria. [Conclusion] It is possible to address scientific questions from the classic ecology to identify the key bacteria during the biodegradation of polycyclic aromatic hydrocarbons compounds by marine microbial ecological networks. Our study discovered close interactions among key bacteria represented by the genera Erythrobacter.

Abstract:Studies on biocontrol of plant diseases mainly focus on interactions among plant, pathogen, and biocontrol agents (BCAs), but ignore the role of associated microbiome of plants. Increasing numbers of studies have revealed the essential roles of plant endophytes, rhizosphere microbiota and phylloplane microflora in resistance to plant diseases. Basing on selected representative reports, we reviewed the composition of plant microbiome, its anti-pathogenic and pathogenic effects for plants, and its effect on pathogenicity of phytopathogen as well as the effect of BCAs on native microbiome. Progress in microbiome researches provides novel perspectives toward plant diseases and biological control, which will help to develop more scientific methods for plant disease management.

Abstract:Termites are efficient lignocellulose degraders in the natural ecosystem. During the long-time evolution, termites have developed different strategies to decompose lignocellulose efficiently with the help of their gut microbiome. Wood-feeding termites have duel-cellulolytic systems that originated from termites and their microbiota. In lower termites, wood particles are digested primarily by endogenous cellulase secreted from the host foregut and midgut and then decomposed almost completely by numerous flagellates in the hindgut of termites. The fermentation products are acetate, carbon dioxide and hydrogen. Wood-feeding higher termites lost flagellates during the evolution. Wood particles are digested primarily by endogenous cellulase secreted from the host and are subsequently degraded by symbiotic bacteria in the hindgut of the termites. Fungus-cultivating termites degrade wood particles with the help of Termitomyces they cultivated in the fungus combs and their intestinal microbiota. The symbiotic microbiota in termite guts may involve in bioprocess like nitrogen fixation and uric acid hydrolyzation, utilization and transformation of metabolic intermediates, and degradation of lignocellulose. It is meaningful to study and imitate the highly efficient lignocellulose-degrading system of termites for biofuel industry development.

Abstract:Traditional Chinese fermented foods, usually produced through fermentation by spontaneously inoculation, are characterized by their special flavors and rich nutrients. The techniques of some traditional fermented foods have thousands of years of history. In recent years, new technologies have been used to explore the mysteries of fermenting processes for traditional fermented foods worldwide, revealing that traditional fermentation systems are valuable to both basic and application research. In this review, we summarize the general features and recent progresses in the microbiome study of traditional Chinese fermented foods, and try to predict the future research directions.

Abstract:[Objective] Characterize classical microscope counting methods, single cell technology and modern molecular methods in determining abundance and composition of total soil microbiome and aerobic methanotrophs in the process of methane oxidation. [Methods] Based on the extracted microbial cells and their DNA (Cell DNA), Single cell DNA, and soil microbiome DNA (Soil DNA), the conventional microscope counting methods and real time quantitive PCR (qPCR) were used to assess the abundance changes of soil microbiome and major aerobic methanotroph groups in aerobic methane oxidation. MiSeq sequencing of 16S rRNA and pmoA genes was used to compare microbial composition changes of soil microbiome and aerobic methanotrophs. [Results] Total microbial abundance in the studied paddy soil obtained by qPCR could be up to 3 orders of magnitude higher than that obtain by microscope counting methods. DAPI staining, CARD-FISH, qPCR of 16S rRNA gene in Cell DNA and Soil DNA showed total microbial abundance (cells/g) were (5.8-7.4)×10⁷, (1.7-1.9)×10⁷, (2.8-6.3)×10⁸, and (1.5-2.7)×10¹⁰, respectively. For methanotrophs, the result of qPCR of Soil DNA is 1.1×10⁷ cells/g which is 3 orders of magnitude higher than that obtained by microscope counting methods. However, all different methods showed that methanotroph abundance increased by 54-fold (CARD-FISH), 388-fold (qPCR of Soil DNA) and 40-fold (qPCR of Cell DNA), respectively, after the soil consumed high-concentration methane. Soil DNA (30 phyla) and Cell DNA (25 phyla) showed similar composition at phylum level by MiSeq sequencing analysis of 16S rRNA genes. More than 95% of the sequences derived from single cell DNA were affiliated to Proteobacteria, though 20 phyla were detected. Furthermore, a similar tendency was found by MiSeq sequencing analysis of pmoA genes in Soil DNA, Cell DNA and Single cell DNA. That is Methylobacter/Methylosarcina of γ-Proteobacteria becoming domaniant genera after high-concentration methane oxidation though, 7 pmoA genotypes existed in the original soil. [Conclusion] Total microbial abundance in the studied paddy soil obtained by microscope counting methods could be 1-3 orders of magnitude lower than that obtained by qPCR. qPCR of 16S rRNA gene in Soil DNA and Cell DNA revealed that the extracted microbial cells constituted only 2% of the total microbial cells in the studied paddy soil. Howerer, the extraction efficiency of methanotrophic cells could be up to 6%. MiSeq sequencing analysis indicated that Cell DNA could reflect the microbiome composition of the paddy soil at phylum level but not genus level as compared to that in Soil DNA, while the single cell sorting technique tended to select for Proteobacteria. These results showed that the resolution of traditional methods and molecular techniques are obviously different, but both methods can well characterize the microbial physiological and ecological processes of methane oxidation in paddy soil. The future study of soil microbiome should pay more attention to the inherent needs of the scientific issues, and to maximize the advantages of different technologies.

Abstract:Recent studies have shown that even in the same population, there might be significant differences among individual cells at both cellular and molecular levels, indicating multiple levels of heterogeneity in microbial cells. Meanwhile, depending on establishing pure culture in the laboratory for the targeted microbes, traditional microbiology approaches are unable to present the original state of microorganisms in natural environments. Moreover, so far only small number of microbial species is cultivated successfully in the laboratory, leaving a great deal of microbial information untouched. Single-cell microbiology can be effective tools for addressing these issues and providing better and in-depth understanding of state of microbial cells. In this mini-review, we briefly introduce the significance of single-cell microbiology, and summarize current state-of-the-art methodologies in this new research area, especially the emerging single-cell omics tools for microbial research.

Abstract:Advances in high-throughput sequencing have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field metagenomics, which is often defined as the analysis of DNA sequences from microbial communities in environmental samples without prior need for culturing. Microbiome data management and analysis have caused concern for microbial researchers because of the dramatic increase of metagenomics data. It has been a research hotspot that how to mine valuable information for further application form such big microbial data. Till now, many metagenomics computational tools and databases have been provided in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and international microbiome projects as well as the platforms for microbial data archiving and analysis, such as Human Microbiome Project (HMP), Earth Microbiome Project (EMP), Metagenomics of Human Intestinal Tract (MetaHIT), MG-RAST, iMicrobe, Integration Microbial Genomes (IMG) and EBI Metagenomics and so on. We also discussed about the basic pipelines and main tools for metagenomics data. Finally, we proposed the necessity of establishing a platform for multi-source microbial data management and bioinformatic analysis.