Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype...
Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with...
The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical...
Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of...
The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we...
This review highlights the benefits of mutualistic plant–microbe interactions in enhancing the resilience of emergent crops and underlies the potential of these crops as valuable resources for exploring novel plant growth-promoting bacteria (PGPB). Emergent crops such as quinoa, amaranth, millet, lupins, hemp and desert truffles exhibit physiological and ecological traits that...
Crop quality is influenced by crop-related factors such as varieties and metabolites, as well as by environmental conditions. Recent studies have shown the important role of rhizosphere microbes in determining crop quality and flavor, but the effects of phyllosphere (aboveground) microbes and metabolites remain unclear. Here, we examined the interaction between phyllosphere...
Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. A total of 280 samples from Campylobacter positive households with complete metadata...
The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers...
The world is facing both an increasingly severe energy crisis and a growing problem of agricultural pollution. The utilization of agricultural waste by anaerobic digestion (AD), has received increasing attention. AD using representative waste cow dung results in total ammonia nitrogen (TAN) accumulation and inhibition of methanogens resulting in reduced CH4 production. However...
The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where...
Previous studies have demonstrated that gut microbiota regulates reproductive performance in mammals. Our prior research identified the gut microbiota-ovary axis as an important contributor to the superior follicular development observed in Chinese indigenous Meishan sows, yet the underlying mechanisms remain unclear. This study aims to elucidate the mechanism through which gut...
The weaning transition from a milk-based to a solid-food diet supports critical developmental changes to the intestinal microbiota and immune system. However, the specific microbial and host features that influence microbial succession at weaning are not well understood. Here, we developed a simple approach to investigate the complex dynamics of microbial succession during...
High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. We developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific long-read amplicons. We focused on the wheat microbiome as a proof-of-principle and...
Microbial communities are increasingly recognized for their essential roles in the reproductive system. However, the microbial communities in healthy gonads—neither in the ovary nor the testis—have not been extensively explored, particularly with respect to sex differentiation. Sex reversal is a unique mode of sex differentiation that is a well-documented phenomenon in various...
Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the...
Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial...
One Health is a concept and framework for addressing the interconnected nature of humans, animals and their environments to improve the health and wellbeing of all three, along with added social and financial benefits. On a microscopic level, the microbiota is a clear biological connector with strains shared across domains (One Health Microbiome). In this review, we introduce the...
Fecal microbiota transplantation (FMT) has emerged as a widely used treatment for various diseases. While previous efforts have focused on selecting “super donors”, the precise modulation of donor microbiota to enhance FMT efficacy remains a critical challenge. This study aimed to develop strategies to modify donor microbiota to promote gastrointestinal development and maturation...
Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbiome-derived metabolites in the human gut, constructed from a controlled feeding experiment of adults on omnivore and enteral nutrition diets. By comparing metabolite concentration before and...
Blue Carbon ecosystems, which include all tidal wetlands, mitigate climate change by capturing and storing carbon dioxide (CO2) from the atmosphere. Most carbon fixation in these systems is thought to be driven by plant and microbial photosynthesis, whereas chemosynthetic processes are assumed to play a minor role. However, these ecosystems often contain anoxic environments ideal...
The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing...
The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity...