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The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal ...
Numerous studies have confirmed a close relationship between the pathogenicity of influenza and respiratory microbiota, but the mechanistic basis for this is poorly defined. Also, the majority of these studies...
High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial compo...
Microbial spoilage in meat impedes the development of sustainable food systems. However, our understanding of the origin of spoilage microbes is limited. Here, we describe a detailed longitudinal study that as...
The immature lungs of very preterm infants are exposed to supraphysiologic oxygen, contributing to bronchopulmonary dysplasia (BPD), a chronic lung disease that is the most common morbidity of prematurity. Whi...
Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resi...
The Correction to this article has been published in Microbiome 2025 13:70
This research aimed to investigate differences in rumen fermentation characteristics between Karakul sheep and Hu sheep reared under identical conditions. The test subjects included newborn Hu and Karakul shee...
The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a pr...
The early colonization and establishment of the microbiome in newborns is a crucial step in the development of the immune system and host metabolism. However, the exact timing of initial microbial colonization...
Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing ...
Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due t...
The Correction to this article has been published in Microbiome 2025 13:55
While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestina...
Alzheimer’s disease (AD) is a prevalent neurodegenerative disease (ND). In recent years, multiple clinical and animal studies have shown that mitochondrial dysfunction may be involved in the pathogenesis of AD...
The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a preva...
The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses...
The growth and health of young ruminants are regulated by their gut microbiome, which can have lifelong consequences. Compared with subjective grouping, phenotypic clustering might be a more comprehensive appr...
Common variable immunodeficiency (CVID) is characterized by hypogammaglobulinemia and recurrent infections. Significant morbidity and mortality are caused by immune dysregulation complications (CVIDid), which ...
Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such ...
The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial...
Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a range of histological findings from the generally benign simple steatosis to steatohepatitis (MASH) which can progress to fibrosis...
The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with th...
The original article was published in Microbiome 2024 12:259
The main application of cork is the production of stoppers for wine bottles. Cork sometimes contains 2,4,6-trichloroanisole, a compound that, at a concentration of ng/L, produces an unpleasant musty odor that ...
Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a signific...
Sponges harbor microbial communities that play crucial roles in host health and ecology. However, the genetic adaptations that enable these symbiotic microorganisms to thrive within the sponge environment are ...
Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow ...
Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut micro...
The complex relationship among sleep, exercise, and the gut microbiome presents a unique opportunity to improve health and wellness. Here, we conducted the first large-scale investigation into the influence of...
The interplay between gut microbiota and immune responses is crucial in ulcerative colitis (UC). Though Akkermansia muciniphila (Akk) shows therapeutic potential, the mechanisms remain unclear. This study sought ...
The Correction to this article has been published in Microbiome 2025 13:54
Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, mic...
Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human...
The overuse of antibiotics has led to lethal multi-antibiotic-resistant microorganisms around the globe, with restricted availability of novel antibiotics. Compared to conventional antibiotics, evolutionarily ...
The application of ‘-omics’ technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplic...
Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. Howev...
Sheep coccidiosis is an infectious parasitic disease that primarily causes diarrhea and growth retardation in young animals, significantly hindering the development of the sheep breeding industry. Cereal grain...
Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how ...
The search for alternatives to antibiotic growth promoters in poultry production has increased interest in probiotics. However, the complexity of the interactions between probiotics, gut microbiome, and the ho...
Correlative structural and chemical imaging of biofilms allows for the combined analysis of microbial identity and metabolism at the microscale. Here, we developed pH-FISH, a method that combines pH ratiometry...
Biological invasions pose an escalating threat to native ecosystems. The accumulation of invasive alien plants worldwide is not saturated yet, underscoring the persistent and growing impact of invasions. Soil ...
Tibetan Plateau is credited as the “Third Pole” after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.
As a globally farmed oyster species, Magallana gigas has garnered significant attention due to the contaminated RNA viruses that have caused illness in humans. However, limited knowledge is available on the bioac...
Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even produ...
Infants exposed to HIV but uninfected have altered immune profiles which include heightened systemic inflammation. The mechanism(s) underlying this phenomenon is unknown. Here, we investigated differences in n...
Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral g...
Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally im...
The Correction to this article has been published in Microbiome 2025 13:7
In recent years, human microbiome research has flourished and has drawn attention from both healthcare professionals and general consumers as the human microbiome is now recognized as having a significant infl...
The original article was published in Microbiome 2024 12:220
The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently ...
The human gut microbiota is inoculated at birth and undergoes a process of assembly and diversification during the first few years of life. Studies in mice and humans have revealed associations between the ear...
The original article was published in Microbiome 2024 12:228
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