Determinants Of Microbial Composition Research Articles

Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples

ObjectiveGrowth in large population-based studies assessing contributions of the gut microbiota to health and disease requires high-throughput sample processing and analysis methods. This study assessed the impact that modifications to a commercially available magnetic bead based, semi-automated DNA extraction kit had on determination of microbial composition, relative to an established in-house method involving a combination of mechanical and chemical lysis. DNA was extracted from faecal samples from healthy adults (n = 12; 34–69 years), microbial composition was determined by V3-V4 16s rRNA sequencing and compared between extraction methods.ResultsDiversity metrics did not differ between extraction methods. Differences in the relative abundance of key phyla, including a significantly lower abundance of the Firmicutes (p = 0.004) and higher relative abundance of the Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.008) phyla were noted where the DNA extraction did not include additional chemical and mechanical lysis. Principal coordinate analysis of family and genera level data also suggested a potential for sample pre-processing to impact microbial composition. Observations of the potential for skewed microbial composition profiles from samples prepared using a semi-automated DNA extraction kit without additional sample pre-processing highlights a need for consideration of standardisation of methodological approaches to increase the comparability of microbial compositional data.

Research Note: Integrated gut microbiome and short-chain fatty acids responds to dominance hierarchy in roosters

The dominant chickens have priority over the use of resources, such as resting places and the announcement of dawn. While cooperation from the subdominant animal is of great help to reduce conflict and maintain the sustainability of a group. However, whether the dominance hierarchy is associated with individuals’ health is not yet known. In this study, we first determined the dominance hierarchy within a group of roosters, to figure out its effects on individuals’ health status by the determination of microbial composition and short-chain fatty acids (SCFAs). Sixteen Weining roosters were kept in a group in order to fix and determine the ranking of dominance hierarchy, as R1 (the highest-ranking rooster), R2, R3, and R4. Results show that the R1 roosters had the highest aggression behavior followed by R2, R3 and R4 (P < 0.05). The alpha diversity of R1, R2, and R4 was higher than R3 roosters (P < 0.05). There were several top 10 phylum and genus microbes among the different ranking roosters (P < 0.05). The acetic acid, propionic acid, butyric acid, and valerate acid concentrations were higher, while isobutyric acid concentration was lower in the higher rank roosters (R1 and R2) than the lower rank roosters, respectively (R3 and R4) (P < 0.05). Our results show that the variation of dominance hierarchy contributes to changes of microbial composition, diversity and metabolites. Dominant roosters seem to benefit from SCFAs activities while subdominant roosters profit from microbial functions.

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population

BackgroundGut microbiota composition is known to depend on environmental (diet, day length, infections, xenobiotic exposure) and lifestyle (alcohol/drug intake, physical activity) factors. All these factors fluctuate seasonally, especially in areas with highly variable climatic conditions between seasons. Seasonal microbiota changes were reported in several previous studies. The purpose of our study was to investigate whether there is a seasonal variability in the gut microbiota composition in Ukrainian population. In contrast to previous studies performed on small-size samples using a longitudinal design, we used cross-sectional design with a large sample size (n = 769). Determination of microbial composition at the level of major microbial phyla was performed by qRT-PCR.ResultsThe relative abundance of major taxonomic groups of gut microbiota was found to be affected by month of sampling. Actinobacteria were more abundant and Bacteroidetes were less abundant in summer-derived samples compared to those obtained during other seasons, whereas Firmicutes content was seasonally independent. The Firmicutes to Bacteroidetes (F/B) ratio was significantly higher in summer-derived samples than in winter-derived ones. Odds to have F/B > 1 were 3.3 times higher in summer samples and 1.9 times higher in autumn samples than in winter ones; neither age, nor sex were significant confounding factors.ConclusionsSeasonality of sampling could influence results of human microbiome research, thereby potentially biasing estimates. This factor must be taken into consideration in further microbiome research.