Predictive functionality of bacteria in naturally fermented milk products of India using PICRUSt2 and Piphillin pipelines

Naturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from MG-RAST/NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction. MUSiCC-normalized KOs and mapped KEGG pathways from both PICRUSt2 and Piphillin resulted in higher percentage of the former in comparison to the latter. Though, functional features were compared from both the pipelines, however, there were significant differences between the predictions. Therefore, a consolidated presentation of both the algorithms presented an overall outlook into the predictive functional profiles associated with the microbiota of the NFM products of India.

Metagenome gene prediction of naturally fermented milk products of India using PICRUSt2 and Piphillin

Background: Naturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction in combination with the commonly used error-corrected denoising programs like DADA2 and Deblur.Results: Significant functional hits were observed from the Piphillin analysis which included some interesting pathways including GABAergic synapse, glutamatergic synapse and serotonergic synapse, which are known to be probiotic-related, among others that are absent in PICRUSt2 analysis. This study also showed the negative correlation of lactic acid bacteria (LAB) members (Lactococcus, Lactobacillus, Leuconostoc) with most of the disease-related functions, which were on the other hand, positively correlated with unwanted contaminants like Staphylococcus, Bacillus and Pseudomonas.Conclusion: The study explored the potential of microbial functional gene prediction using PICRUSt2 and Piphillin software, and indicated the significance of the presence of LAB in these NFM products of India. Since most LAB members are known to be potential health-promoting bacteria, their negative correlation to many of the disease-related functions also indicates their role in combatting unwanted potential contaminants.

Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.

Patterns of Denitrification and Methanogenesis Rates from Vernal Pools in a Temperate Forest Driven by Seasonal, Microbial Functional Gene Abundances, and Soil Chemistry

Due to their relatively small sizes, temperate forest vernal pools are less studied than other wetlands, despite being potential biogeochemical hotspots in landscapes. We investigated spatial and temporal factors driving N2O and CH4 emission rates from vernal pools in a temperate forest. We determined higher N2O (3.66 ± 0.53 × 10−6, μg N2O/m2/h) and CH4 (2.10 ± 0.7 × 10−3, μg N2O/m2/h) rates in spring relative to fall (~50% and 77% lower for N2O and CH4 rates, respectively) and winter (~70% and 94% lower for N2O and CH4 rates, respectively). Soil organic matter, nitrate content and bacterial 16S rDNA, nirS, and norB gene abundances emerged as significant drivers of N2O rates, whereas, soil pH, organic matter content and mcrA abundance were significant drivers of CH4 rates. Denitrification gene abundances were negatively correlated with N2O rates, whereas mcrA abundance correlated positively with CH4 rates. Results suggest that CH4 rates may be directly coupled to methanogen abundance, whereas N2O rates may be directly impacted by a variety of abiotic variables and indirectly coupled to the abundance of potential denitrifier assemblages. Overall, additional studies examining these dynamics over extended periods are needed to provide more insights into their control.