State-of-the-Art Clinical Microbiology in South Korea: Current Trends and Future Prospects

Researchers and clinicians have repeatedly explored the clinical aspects of microorganisms because the human body is inhabited by several different microbial species and their strains [...]

Evolutionary Ecology of Natural Comammox Nitrospira Populations

Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease

Background The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent that and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits. Methods We performed 16S rRNA gene sequencing on stool from 1423 participants of the FHS Generation 3, OMNI2, and New Offspring Spouse cohorts. Data processing and taxonomic assignment were performed with the 16S bioBakery workflow using the UPARSE pipeline. We conducted statistical analyses to investigate trends in overall microbiome composition and diversity in relation to disease states and systematically examined taxonomic associations with a variety of clinical traits, disease phenotypes, clinical blood markers, and medications. Results We demonstrate that overall microbial diversity decreases with increasing 10-year CVD risk and body mass index measures. We link lifestyle factors, especially diet and exercise, to microbial diversity. Our association analyses reveal both known and unreported microbial associations with CVD and diabetes, related prescription medications, as well as many anthropometric and blood test measurements. In particular, we observe a set of microbial species that demonstrate significant associations with CVD risk, metabolic syndrome, and type 2 diabetes as well as a number of shared associations between microbial species and cardiometabolic subphenotypes. Conclusions The identification of significant microbial taxa associated with prevalent CVD and diabetes, as well as risk for developing CVD, adds to increasing evidence that the microbiome may contribute to CVD pathogenesis. Our findings support new hypothesis generation around shared microbe-mediated mechanisms that influence metabolic syndrome, diabetes, and CVD risk. Further investigation of the gut microbiomes of CVD patients in a targeted manner may elucidate microbial mechanisms with diagnostic and therapeutic implications.

The Impact of Selenium on the Rhizosphere Microbiome of a Hyperaccumulation Plant Cardamine Violifolia

Cardamine violifolia is the only selenium hyperaccumulation plant found in China. It has been developed as a source of medicinal and edible products for selenium supplementation of human. It is essential to increase selenium content of C. violifolia for nutrient biofortification and many planting approaches have been developed to achieve this aim. However, the contribution of rhizosphere microbes of C. violifolia to the selenium enrichment has not been investigated. In this study, four types of selenium, i.e., selenate, selenite, nanoparticles element selenium from Bacillus subtilis, and organic selenium from yeast, was added to the soil for the growth of C. violifolia, respectively. Selenate had the highest accumulation in C. violifolia, following by selenite, B. subtilis-Se, and yeast-Se. Except for yeast-Se, the concentration of selenium in C. violifolia is positively correlated with the amount of selenium added in the soil. Furthermore, different exogenous selenium exhibited distinct effects on the rhizosphere microbiome of C. violifolia. Both Alpha diversity and Beta diversity analyses displayed that rhizosphere microbiome were more obviously affected by selenium from B. subtilis and yeast than that of selenate and selenite. Different microbial species were enriched in the rhizosphere of C. violifolia under various exogenous selenium treatments. B. subtilis-Se application enhanced the abundance of Leucobacter, Sporosarcina, Patulibacter, and Denitrobacter, and Yeast-Se application enriched the abundance of Singulishaera, Lactobacillus, Bdellovirio, and Bosea. Bosea and the taxon belonging to the order of Solirubrobacterales was enriched in the samples with selenite and selenite addition, respectively, and their abundance was linearly related to the concentration of selenate and selenite application in the rhizosphere of C. violifolia. In summary, this study revealed the response of the rhizosphere microbiome of C. violifolia to exogenous selenium and it is of help to develop suitable selenium fertilizers to increase selenium hyperaccumulation level of this plant.

From Past to Present: Biotechnology in Mexico Using Algae and Fungi

Algae and fungi share a rich history in the fields of basic and applied natural science. In biotechnology, in particular, algae and fungi are of paramount importance, due to the production and development of valuable compounds, such as pharmaceuticals, enzymes, and biofuels. They are also used in waste fermentation, biocontrol of pathogens, and food processing and improvement, among other fields. Although a substantial number of different microorganisms are utilized for these purposes, there lies tremendous potential in uncharacterized microbial species. For this reason, biodiversity hotspots offer a wealth of potential in the discovery of new products and processing strategies based on these microorganisms. This review presents an overview of the use of algae and fungi in pre-Hispanic times/modern-day Mexico for the benefits of mankind. One of our objectives is to raise awareness about the potential of developing research projects for identification and biotechnological utilization of algae and fungi in a megadiverse country, such as Mexico.

Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Making full use of high fiber and low-cost crop coproducts is helpful to alleviate the situation of people and livestock competing for crops. Digestion of dietary fibers in pigs is mainly through microbial fermentation in the large intestine. To reveal microbiota related to fiber digestion in pigs, fecal samples have been collected from 274 healthy female Suhuai pigs at 160 days of age under the same feeding conditions and have measured apparent neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility. Samples from Suhuai pigs with extreme high and low apparent NDF digestibility and extreme high and low apparent ADF digestibility were subjected to shotgun metagenomic sequencing. At the species level, 62 microbial species in H_NDF group and 54 microbial species in H_ADF group were related to high fiber digestibility. Among them, Lachnospiraceae bacterium 3-1 and Alistipes sp. CAG:514 may be new types of microorganisms associated with fiber digestion. In addition, we found that more abundant GH5 and GH48 family (contribute to cellulose degradation) genes, GH39 and GH53 family (contribute to hemicellulose degradation) genes in microorganisms may contribute to the higher apparent NDF digestibility of pigs, and more abundant GH3 and GH9 family (contribute to cellulose degradation) genes in microorganisms may contribute to the higher apparent ADF digestibility of pigs. The abundance of AA4 family (helps in lignin degradation) genes in H_NDF and H_ADF groups was significantly higher than that in L_NDF and L_ADF groups, respectively (P < 0.05). Three pathways in H_NDF group and four pathways in H_ADF group are important pathways associated with degradation of non-starch polysaccharides, and their relative abundance is significantly higher than that in L_NDF and L_ADF groups, respectively. Gut microbiota of Suhuai pigs with high apparent fiber digestibility had higher abundance of genes and microbiota related to fiber digestion and may have stronger fiber digestion potential compared with low apparent fiber digestibility group. This study revealed that the characteristics of gut microbiota and microbial gene functions of pigs with high fiber apparent digestibility, which provided a theoretical basis and reference for further understanding the impact of gut microbiota on fiber digestibility of pigs.