Shifts in structure and function of bacterial community in river and fish pond sediments after a phenol spill

Phenol is widely used in industrial processes and has microbial toxicity. However, the effects of a phenol spill on the microbial community are not clear. The present study explored the changes of bacterial communities in river and fish pond sediments after a phenol spill. The bacterial richness and diversity in river sediments were lower on day 30 (36 days after the spill) than on day 0, while they increased in fish pond sediments. The structures and functions of bacterial communities in both river and fish pond sediments were changed, and a more dramatical variation was detected in fish pond sediments. In river sediments, Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Nitrospirae were the major bacterial phyla, and Chloroflexi was enriched. In fish pond sediments, genera Brevibacillus dominated bacterial communities initially, and bacterial composition showed a dramatic change on day 30. Most predicted metabolism functions, as well as genetic information processing functions of translation, replication, and repair, were enhanced in both river and fish pond sediments, while they showed an opposite change trend for xenobiotic degradation function. This work could strengthen our understanding of the effects of phenol spills on sediment bacterial communities in both lotic and lentic ecosystems.

Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations

BACKGROUND

The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period. Soil samples at two-months intervals were collected and analyzed.

RESULTS

The results of the enzyme activities revealed that acid phosphatase, arylsulfatase, β-glucosidase, and urease activities differed considerably among the soils representing the three management practices. Combining the redundancy and multiple regression analysis, the change in the arylsulfatase activity was explained by soil pH as a significant predictor in the SA soils. The soil bacterial community was predominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes in the soil throughout the sampling period. Higher Alpha diversity scores indicated increased bacterial abundance and diversity in the SA soils. A significant relationship between bacterial richness indices (SOBS, Chao and ACE) and soil pH, K and, P was observed in the SA soils. The diversity indices namely Shannon and Simpson also showed variations, suggesting the shift in the diversity of less abundant and more common species. Furthermore, the agricultural management practices, soil pH fluctuation, and the extractable elements had a greater influence on bacterial structure than that of temporal change.

CONCLUSIONS

Based on the cross-over analysis of the bacterial composition, enzymatic activity, and soil properties, the relationship between bacterial composition and biologically-driven ecological processes can be identified as indicators of sustainability for the tea plantation.

Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BACKGROUND

Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities.

RESULTS

In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial.

CONCLUSIONS

Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

Synergistic and antagonistic interactions between antibiotics and synbiotics in modifying the murine fecal microbiome

Purpose

Pro- and synbiotics have been reported to ameliorate the adverse (dysbiotic) effects of antibiotics on the gut microbial architecture, but little is known how synbiotics and antibiotics interact with each other in shaping the gut microbiota. To explore this mutual interaction we examined, first, the effect of a multi-strain synbiotic on antibiotic-induced dysbiosis and, second, the dysbiotic effect of antibiotics followed by prolonged synbiotic exposure.

Methods

The synbiotic containing nine bacterial strains was administered to male mice via the drinking water, while the antibiotic mix containing bacitracin, meropenem, neomycin, and vancomycin was administered via oral gavage. Two experimental protocols were used. In protocol 1, mice were administered placebo or synbiotic for 3 weeks prior to and during an 11-day vehicle or antibiotic treatment. In protocol 2 the synbiotic was administered for a prolonged period of time, starting 3 weeks prior and continuing for 12 weeks after an 11-day vehicle or antibiotic treatment. Subsequently, the fecal microbiome was analyzed by 16S rRNA sequencing using oligonucleotide primers 16s_515_S3_fwd: GATTGCCAGCAGCCGCGGTAA and 16s_806_S2_rev: GGACTACCAGGGTATCTAAT followed by sequencing using the Ion Torrent One. The final sequence files were analyzed by QIIME 1.8 workflow scripts.

Results

Antibiotic treatment markedly decreased the bacterial richness and diversity of the fecal microbiota. Synbiotic administration for 3 weeks prior to and during an 11-day antibiotic treatment preserved the Lactobacillales and expanded the Verrucomicrobiales and Bifidobacteriales order, but did not prevent the depletion of Bacteroidales and the short-term proliferation of Enterobacteriales. When the synbiotic administration was continued for 12 weeks after the end of antibiotic treatment, the rise of Verrucomicrobiales was maintained, whereas the preservation of Lactobacillales and boost of Bifidobacteriales was lost. The abundance of Clostridiales was enhanced by long-term synbiotic treatment after short-term exposure to antibiotics, while the antibiotic-depleted Bacteroidales underwent a delayed recovery.

Conclusions

There are complex synergistic and antagonistic interactions of synbiotics and antibiotics in influencing distinct bacterial orders of the fecal microbiota. The impact of a short-term antibiotic exposure is profoundly different when analyzed after synbiotic pretreatment or following prolonged synbiotic administration in the post-antibiotic period.

Bacterial community shaped by heavy metals and contributing to health risks in cornfields

Scientists are increasingly aware that heavy metal contamination in soils, especially in farmland ecosystems, can negatively affect human health and alter the bacterial community that plays a critical role in plant growth and heavy metal accumulation. The goal of the present paper was to uncover how various heavy metals and non-metallic elements affect human health and bacterial diversity in cornfields and to explore the contribution of soil bacteria to heavy metal accumulation in crops. Soil samples were collected from five counties in Shandong Province, China, where abnormally high levels of heavy metals and metalloids were caused by mining and heavy industry. We calculated a hazard quotient (HQ) to evaluate the health risk these heavy metals cause and analyzed the soil bacterial community using 16S rRNA gene sequencing. The HQ results showed that As posed the greatest threat to human health followed by Pb although concentrations of all metals did not reach the health risk threshold. Meanwhile, principal component analysis (PCA) and redundancy analysis (RDA) revealed soil bacterial richness was significantly influenced by As, Ni, and Cr as well as pH and phosphorus, but not by the species diversity of aboveground weeds. The most abundant bacteria in our study region were heavy metal tolerant groups, specifically Actinobacteria and Proteobacteria. Moreover, correlation analysis suggested that Actinobacteria might reduce the phytoaccumulation of Cr, Cu, Zn, and Hg in corn, while Proteobacteria might weaken phytoaccumulation of Pb, Ni, As, and Cd. Our results verified that heavy metals play an important role in shaping the soil bacterial community. Using native bacteria in farmland provides a potential biological strategy for reducing the health risk posed by heavy metals related to food consumption.