microbial ecology
Research Article | Host-Microbe BiologyA Framework for Effective Application of Machine Learning to Microbiome-Based Classification ProblemsDiagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML...
Research Article | Applied and Environmental ScienceProkaryotic and Viral Community Composition of Freshwater Springs in Florida, USAAquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate...
Research Article | Host-Microbe BiologyInfluence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom ComparisonGlobal microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly...
Commentary | Ecological and Evolutionary ScienceMicrobial Life Deep UnderfootSoil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored.
Research Article | Ecological and Evolutionary ScienceMaintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial BacteriaDue to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit...
Editor's Pick Research Article | Ecological and Evolutionary ScienceEcological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil HorizonsSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly...
Author Reply | Applied and Environmental ScienceReply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
Research Article | Ecological and Evolutionary ScienceMicrobial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial SignaturesHumans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the “microbial signatures” they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that...
Observation | Host-Microbe BiologyFecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community StructureConsidering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals...
Research Article | Clinical Science and EpidemiologyThe Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western KenyaThe gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is...