Microbiome definition re-visited: old concepts and new challenges
The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fi...Microbiome 2020 8:103Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys
Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-tem...Microbiome 2020 8:102Correction to: The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts
An amendment to this paper has been published and can be accessed via the original article.Microbiome 2020 8:101The original article was published in Microbiome 2020 8:71Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants
Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little informati...Microbiome 2020 8:100Reservoirs of antimicrobial resistance genes in retail raw milk
It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw ...Microbiome 2020 8:99Developing standards for the microbiome field
Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited o...Microbiome 2020 8:98A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes
Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponge...Microbiome 2020 8:97Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites
Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humif...Microbiome 2020 8:96Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation
The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied ...Microbiome 2020 8:95Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments
Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methan...Microbiome 2020 8:94The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differ...Microbiome 2020 8:93Climate mediates continental scale patterns of stream microbial functional diversity
Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce ...Microbiome 2020 8:92Topography of the respiratory tract bacterial microbiota in cattle
Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has rece...Microbiome 2020 8:91VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart com...Microbiome 2020 8:90Depth-related variability in viral communities in highly stratified sulfidic mine tailings
Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial fir...Microbiome 2020 8:89Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease
Bacteroides thetaiotaomicron (Bt) is a prominent member of the human intestinal microbiota that, like all gram-negative bacteria, naturally generates nanosized outer membrane vesicles (OMVs) which bud off from th...Microbiome 2020 8:88Re-evaluating the relationship between missing heritability and the microbiome
Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including th...Microbiome 2020 8:87Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations
Inanimate surfaces within a hospital serve as a reservoir of microbial life that may colonize patients and ultimately result in healthcare associated infections (HAIs). Critically ill patients in intensive car...Microbiome 2020 8:86Skin microbiota analysis-inspired development of novel anti-infectives
The alarming spread of antimicrobial resistance requires the development of novel anti-infective drugs. Despite the recent research focus on the human microbiome and its likely value to understand and exploit ...Microbiome 2020 8:85Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria
In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understandi...Microbiome 2020 8:84Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models
The anti-inflammatory property of ω-3 polyunsaturated fatty acids (PUFA) has been exploited in the management of inflammatory bowel disease (IBD) with promising results. However, it remains unclear if PUFA pla...Microbiome 2020 8:83Earth microbial co-occurrence network reveals interconnection pattern across microbiomes
Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but thei...Microbiome 2020 8:82Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation
Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and c...Microbiome 2020 8:81Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing
High-throughput sequencing of bacterial 16S rRNA gene (16S-seq) is a useful and common method for studying bacterial community structures. However, contamination of the 16S rRNA genes from the mitochondrion an...Microbiome 2020 8:80Using soil bacterial communities to predict physico-chemical variables and soil quality
Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial commun...Microbiome 2020 8:79Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms
Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies h...Microbiome 2020 8:78Correction to: Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics
An amendment to this paper has been published and can be accessed via the original article.Microbiome 2020 8:77The original article was published in Microbiome 2020 8:47Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzym...Microbiome 2020 8:76Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes
Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, inc...Microbiome 2020 8:75Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria
Gut microbiome alterations are closely related to human health and linked to a variety of diseases. Although great efforts have been made to understand the risk factors for multiple myeloma (MM), little is kno...Microbiome 2020 8:74Correction to: Genetic and metabolic links between the murine microbiome and memory
An amendment to this paper has been published and can be accessed via the original article.Microbiome 2020 8:73The original article was published in Microbiome 2020 8:53No evidence for Wolbachia as a nutritional co-obligate endosymbiont in the aphid Pentalonia nigronervosa
Obligate symbiotic associations are present in a wide variety of animals with a nutrient-restricted diet. Aphids (hemiptera: Aphididae) almost-universally host Buchnera aphidicola bacteria in specialised organs (...Microbiome 2020 8:72The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts
Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial commun...Microbiome 2020 8:71The Correction to this article has been published in Microbiome 2020 8:101Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest
The phyllosphere is an important microbial habitat, but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plan...Microbiome 2020 8:70Gut microbiota-derived indole 3-propionic acid protects against radiation toxicity via retaining acyl-CoA-binding protein
We have proved fecal microbiota transplantation (FMT) is an efficacious remedy to mitigate acute radiation syndrome (ARS); however, the mechanisms remain incompletely characterized. Here, we aimed to tease apa...Microbiome 2020 8:69Temporal transcriptional patterns of cyanophage genes suggest synchronized infection of cyanobacteria in the oceans
Based on the peak expression times during infection, early, middle, and late genes have been characterized in viruses (cyanophages) that infect the unicellular cyanobacterium Prochlorococcus. Laboratory experimen...Microbiome 2020 8:68Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse
Mounting evidence suggests a role for the gut microbiota in modulating brain physiology and behaviour, through bi-directional communication, along the gut-brain axis. As such, the gut microbiota represents a p...Microbiome 2020 8:67Correction to: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming
An amendment to this paper has been published and can be accessed via the original article.Microbiome 2020 8:66The original article was published in Microbiome 2018 6:14Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequ...Microbiome 2020 8:65Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance
Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and mana...Microbiome 2020 8:64A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals
In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group ...Microbiome 2020 8:63Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome
The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we...Microbiome 2020 8:62The neovaginal microbiome of transgender women post-gender reassignment surgery
Gender reassignment surgery is a procedure some transgender women (TW) undergo for gender-affirming purposes. This often includes the construction of a neovagina using existing penile and scrotal tissue and/or...Microbiome 2020 8:61Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts
The multifaceted interactions between gastrointestinal (GI) helminth parasites, host gut microbiota and immune system are emerging as a key area of research within the field of host-parasite relationships. In ...Microbiome 2020 8:60Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
The chaperone ClpB, a bacterial protein, is a conformational antigen-mimetic of α-melanocyte-stimulating hormone (α-MSH) implicated in body weight regulation in mice. We here investigated the potential associa...Microbiome 2020 8:59Isolation and characterization of diverse microbial representatives from the human skin microbiome
The skin micro-environment varies across the body, but all sites are host to microorganisms that can impact skin health. Some of these organisms are true commensals which colonize a unique niche on the skin, w...Microbiome 2020 8:58Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima
Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While...Microbiome 2020 8:57
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