Read the full paper: Shifts in vegetation impact estuary microbiomes

Published in mSystems

The mgtC gene encodes an inner membrane protein that has been horizontally acquired by multiple bacterial species, including several mammalian pathogens. In Salmonella enterica, MgtC promotes replication in mammalian macrophages and allows this bacterium to survive cytoplasmic magnesium (Mg2+) starvation. These phenotypes are thought to result from MgtC’s inhibition of Pi metabolism and adenosine triphosphate (ATP) production, which prevents the accumulation of toxic levels of Mg2+-chelating ATP and disrupts other physiological processes that depend strictly on Mg2+, such as ribosome assembly and translation. In the current study, we show that processes that are controlled by MgtC vary with the genetic and biochemical contexts in which this protein is expressed. While establishing a broader role for MgtC as a regulator, our findings illustrate how horizontally acquired regulatory genes can potentiate regulatory interactions, facilitating the evolution of new traits.

Coastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerab...

Published in mSystems

Oxytricha species are widely distributed in freshwater and terrestrial ecosystems, playing significant ecological roles in microbial communities. Their ability to undergo encystment provides a powerfu...

Efforts to connect the structure of microbial communities with environmental processes and host health have captured widespread interest among scientists and the general public. The methods used to generate the sequencing data that are fundamental to these efforts result in wide variation in the number of sequences per sample. This variation and how to account for it can have detrimental effects on the ability to draw valid conclusions. Compositional data analysis methods, including robust Aitchison principal component analysis (PCA), have grown in popularity for mitigating these effects and have been proposed as alternatives to rarefaction. In this study, I reviewed and fixed the code that was used to benchmark robust Aitchison PCA and expanded the analysis. With this improved and expanded analysis, I found that rarefaction was still superior to robust Aitchison PCA and other methods of controlling for uneven sequencing effort.

Colorectal cancer does not develop in a single way, and different tumor types may interact differently with bacteria living on the bowel lining. This study examined both tissue-associated bacteria and DNA methylation, an epigenetic mark that helps regulate genes, in paired tumor and nearby non-tumor...

The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for d...

In this study, we used a new method of detecting active viruses that lyse (kill) their microorganism hosts in soil. We accomplished this by tracing “heavy” versions of carbon from soil microorganisms ...

Soil-transmitted helminths (STHs) refer to a group of parasitic nematode worms that infect humans and are transmitted primarily via soil contaminated with eggs or larvae passed in the feces of infected individuals. The STH species include Ascaris lumbricoides (roundworm), Trichuris trichiura (whipworm), Ancylostoma duodenale, and Necator americanus (hookworms), and Strongyloides stercoralis. Globally, these infections remain among the most prevalent neglected tropical diseases, affecting an estimated 1.5 billion people, or ~24% of the world’s population, predominantly in low- and middle-income countries (1). Among these, A. lumbricoides and T. trichiura contribute substantially to the global burden, with an estimated 772–892 million and 429–508 million infections, respectively (1, 2).

In this work, we describe a targeted phage discovery method that allows immediate isolation of phages with specific traits. Currently, to find a phage with specific properties, huge libraries of phage...

Diet is a key determinant of gut microbial composition and mucosal immune function, yet the microbial mechanisms linking diet-mediated metabolic changes to immune regulation remain incompletely understood. T helper 17 (Th17) cells play central roles in both protective mucosal immunity and inflammatory pathology, making them a critical target of immunometabolic regulation. In this study, we show that 1,3-butanediol (BD) treatment, which leads to elevated circulating β-hydroxybutyrate (BHB) independently of diet, is associated with suppression of intestinal Th17 responses, remodeling of the gut microbiota, and reduced levels of segmented filamentous bacteria (SFB). We further demonstrate that BHB-associated microbiota changes are linked to increased susceptibility to enteric infection. This work provides a mechanistic framework illustrating how metabolic state can influence host immunity through selective effects on commensal microbes. These findings inform future studies of microbiota-mediated immune regulation.

University of Missouri researchers are using artificial intelligence to uncover hidden clues among the trillions of bacteria living in the human gut, including changes that could one day help scientists detect diseases earlier. The Mizzou team—which brings together expertise in medicine, data science and engineering—developed a new machine-learning tool capable of finding biological signals that conventional methods miss. Their paper is published in the journal mSystems.

Mounting global responses to dynamic environmental conditions is a crucial function that bacterial cells must perform. Global regulatory networks are most often studied in individual species, however,...

Many microbial genes have no experimentally established function, limiting our ability to explain how microorganisms adapt to their environments. We examined this uncharacterized gene space, or “unkno...

Prescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how r...

Prescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how repeated burning influences soil biological properties—including the functional role that soil microorganisms play in nutrient cycling and greenhouse gas production. We addressed this gap by studying soils from the Albany Pine Bush, a rare and endangered ecosystem that has experienced regular prescribed fires for 30 years. Long-term fire management significantly altered soil chemistry, specifically lowering the amount of nitrogen in the soil. In addition, we found that fire management decreased the genetic potential of the soil microbial community to produce nitrogen oxides—potent contributors to climate change. Thus, prescribed fire’s contribution to greenhouse gas emissions may involve a complex relationship between direct fire-driven emissions, increased fire resilience of promoted vegetation, and—as suggested by our results—the reduced ability of soil microbes to produce greenhouse gases.

Read the full paper: Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries

A common theme for life across complex scales and diverse habitats and ecologies is the “fight” for survival. For some organisms, this fight will involve developing strategies that allow them to cope ...

Many microbial genes have no experimentally established function, limiting our ability to explain how microorganisms adapt to their environments. We examined this uncharacterized gene space, or “unknome” in SAR11, the most abundant bacterial clade in the ocean, by integrating evolutionary conservation, genomic context, predicted protein structure, and environmental distribution. This approach enabled us to prioritize components of the SAR11 unknome, including a core unknome conserved across the clade and genes enriched in specific lineages, and to identify several candidates with possible ecological roles in nutrient acquisition and defense against viruses. Our results suggest that the SAR11 unknome contains important clues to the ecological success of SAR11 rather than merely reflecting incomplete annotation or gene-prediction artifacts. Our study highlights the potential value of unknome analysis for identifying ecologically relevant genes in environmental microorganisms.

The trillions of bacteria living in the human digestive tract may play a decisive role in determining whether an individual can successfully lose weight, according to research published this week in mSystems, a journal of the American Society for Microbiology. Researchers at the Institute for Systems Biology in Seattle identified specific genetic signatures in the gut microbiome that were predictive of weight loss response in a cohort of individuals participating in a commercial wellness program.

Pediatric short bowel syndrome (SBS) is a primary cause of intestinal failure, yet prior research characterizing the gut microbiota has focused almost exclusively on bacteria. In this study, we charac...

Bacteria and their viruses (phages) are locked in perpetual evolutionary conflict. Some bacteria harbor phage satellites, specialized parasites that are activated to hijack the phage’s components to s...

Isoprenoid quinones are small electron-carrying molecules found in the membranes of organisms that produce energy through photosynthesis or respiration and participate in other important cellular processes. Recent advances in the characterization of their biosynthesis pathways enable their automated annotation from genome analyses. In this article, we performed the genomic analysis of over 26,000 cultured and uncultured bacteria, which was complemented by literature data compiled on over 6,000 cultured bacteria. This enabled us to provide an unprecedented overview of quinone distribution across the bacterial diversity. Creating such a comprehensive data set revealed new information about quinone distribution and evolutionary paths and will facilitate future exploration of various aspects of quinone biology, including their role in the evolution and diversification of bacterial metabolism.