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The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown.
Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and...
Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT ...
Although short-term high-fat diet (S-HFD) and long-term high-fat diet (L-HFD) induce metabolic disorder, the underlying epigenetic mechanism is still unclear.
The original article was published in Microbiome 2025 13:51
The responses of the infant gut microbiota to infection significantly disrupt the natural intrahost evolutionary processes of the microbiome. Here, we collected a 16-month longitudinal cohort of infant gut mic...
Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes ...
The original article was published in Microbiome 2025 13:23
Approximately, one-third of dairy cows suffer from postpartum diseases. Ketosis is considered an important inducer of other postpartum diseases by disrupting energy metabolism. Although the rumen microbiome ma...
Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 ...
Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infec...
The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The...
As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowled...
The microbiome is a complex ecosystem of interdependent taxa that has traditionally been studied through cross-sectional studies. However, longitudinal microbiome studies are becoming increasingly popular. The...
Wild rodents and shrews serve as vital sentinel species for monitoring zoonotic viruses due to their close interaction with human environments and role as natural reservoirs for diverse viral pathogens. Althou...
The complex interactions between host genetics and the gut microbiome are well documented. However, the specific impacts of gene expression patterns and microbial composition on each other remain to be further...
Promoting resistance to enteric pathogen infection is a core function of the gut microbiota; however, many of the specific host–commensal interactions that mediate this protection remain uncharacterised. To ad...
Fecal abundances of Enterobacteriaceae and Enterococcaceae are elevated in patients following Roux-en-Y gastric bypass (RYGB) surgery. Concurrently, fecal concentrations of tyramine, derived from gut bacterial me...
In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be di...
In the oral cavity, host-microbe interactions (HMI) continuously occur and greatly impact oral health. In contrast to the well-studied disease-associated HMI during, for example, periodontitis, HMI that are es...
The emergence of tick-borne pathogens poses a serious threat to both human and animal health. There remains controversy about virome diversity in relation to tick genus and ecogeographical factors.
Gut microbiota-derived urolithins may influence multiple myeloma (MM) disease progression and treatment. We analyzed urolithins and their associated microbiota in a retrospective cohort of 45 patients with act...
The original article was published in Microbiome 2025 13:18
The original article was published in Microbiome 2024 12:275
The original article was published in Microbiome 2024 12:88
Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027...
Cytotoxic T-lymphocyte-associated protein 4 deficiency (CTLA4-D) is an inborn error of immunity (IEI) caused by heterozygous mutations, and characterized by immune cell infiltration into the gut and other orga...
The Correction to this article has been published in Microbiome 2025 13:74
Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to underst...
At an early age, chickens commonly exhibit a rise in the average daily gain, which declines as they age. Further studies indicated that the decrease in chicken growth performance at a later age is closely asso...
Altered gut microbiota has emerged as a major contributing factor to the etiology of chronic conditions in humans. Antibiotic exposure, historically dating back to the mass production of penicillin in the earl...
The original article was published in Microbiome 2024 12:232
Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the ...
Weaning-associated enteric diseases are a major concern in the swine industry. This study investigates the effects of fecal microbiota transplantation (FMT) on the jejunum of weanling piglets, a segment of bow...
Synthetic human milk oligosaccharides (HMOs) are used to supplement infant formula despite limited understanding of their impact on the post-weaned developing gut microbiota. Here, we assess the influence of 0...
Microbial eukaryotes play a crucial role in biochemical cycles and aquatic trophic food webs. Their taxonomic and functional diversity are increasingly well described due to recent advances in sequencing techn...
Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibioti...
The China Space Station (CSS) modules feature many areas that are difficult to clean and thus susceptible to microbial outbreaks. A new sampling method utilizing an equivalent material sheet was applied to cha...
The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco...
Antimicrobial toxin genes (ATGs) encode potent antimicrobial weapons in nature that rival antibiotics, significantly impacting microbial survival and offering potential benefits for human health. However, the ...
The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequen...
Microbiome amplicon sequencing data are distorted by multiple protocol-dependent biases from bacterial DNA extraction, contamination, sequence errors, and chimeras, hindering clinical microbiome applications. ...
Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do,...
Disorder in bile acid (BA) metabolism is known to be an important factor contributing to diarrhea. However, the pathogenesis of BA disorder-induced diarrhea remains unclear.
A growing body of evidence demonstrates that host-associated microbial communities of plant leaf surfaces (i.e. the phyllosphere) can influence host functional traits. However, it remains unclear whether host ...
The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of pro...
Root exudates serve as chemical signaling molecules that regulate rhizosphere interactions and control soil-borne diseases. The interactions between plants and the soil microbiome play dynamic and crucial role...
Gut microbiota has been extensively demonstrated to modulate host lipid metabolism. Higher intramuscular fat (IMF) accumulation in Chinese indigenous breed pigs is associated with their special gut microbiota ...
The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions...
Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective...
Genital inflammation increases HIV susceptibility and is associated with the density of pro-inflammatory anaerobes in the vagina and coronal sulcus. The penile urethra is a critical site of HIV acquisition, al...
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