Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.
Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem
Modulation of genotoxic enzyme activities by non-digestible oligosaccharide metabolism in in-vitro human gut bacterial ecosystems
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
Host-microbe symbiosis: the squid-Vibrio association--a naturally occurring, experimental model of animal/bacterial partnerships
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean
Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics
RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
The secret languages of coevolved symbioses: insights from the Euprymna scolopes-Vibrio fischeri symbiosis
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
Associating microbiome composition with environmental covariates using generalized UniFrac distances
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization
Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study
Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
Metabarcoding Analysis of Phytophthora Diversity Using Genus-Specific Primers and 454 Pyrosequencing
Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome
Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria
Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach
Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks
Determining the quality and complexity of next-generation sequencing data without a reference genome
Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems
The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers
Fermentation of Dietetic Fiber from Green Bean and Prickly Pear Shell by Pure and Mixture Culture of Lactobacillus acidophilus LA-5 and Bifidobacterium bifidum 450B
Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities
Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome
Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants
The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study
Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil
Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa
Integrated 'omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture
Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples
Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach
Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale
Symposium review: The uterine microbiome associated with the development of uterine disease in dairy cows
Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research
Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies
Constructing personalized longitudinal holo'omes of colon cancer-prone humans and their modeling in flies and mice
Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization.
HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function
Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation
A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle
Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations
metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data
Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling
Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities
Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle
Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota
Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea
Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture.
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