Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

Investigating spatial and temporal dynamics in microbial community composition of multiple full-scale slow sand filters in drinking water treatment

Slow sand filters (SSFs) are essential for producing high-quality and sustainable drinking water, relying on chemical, physical, and microbial processes to remove nutrients, organic matter, and pathogens. Despite numerous studies on the physical and chemical mechanisms in SSFs, the microbial processes and dynamics remain poorly understood. This study bridges this knowledge gap by investigating the spatial and temporal dynamics of prokaryotic communities within SSFs, by analysing different depths and the top layer, the Schmutzdecke (SCM), over time in full-scale SSFs from different drinking water treatment plants in The Netherlands. Utilising 16S ribosomal RNA gene-targeted amplicon sequencing and quantitative PCR, we observed a horizontally uniform prokaryotic community at each depth at all analysed SSFs, suggesting effective influent water and nutrient distribution, regardless of filter size or influent inlet design. Vertically, however, the prokaryotic composition varied significantly, with the SCM showing higher biomass and diversity compared to the deeper layers. This study identified a core prokaryotic community, including the families Nitrospiraceae, Pirellulaceae, Nitrosomonadaceae, Gemmataceae, and Vicinamibacteriaceae, consistent across various depths and SSFs, and in the SCMs of different ages. Their presence suggests a central role in supporting key biological processes in SSFs such as organic matter degradation and nitrification. Additionally, the relative abundance of archaea increased with sand depth in all SSFs, suggesting their adaptation to lower-nutrient conditions found in deeper layers. Analysis of the SCM over time showed that after scraping, the prokaryotic community gradually adapted, with minimal biomass increase during the first 3.6 years, eventually evolving into a mature, diverse, and even prokaryotic community. Our findings highlight the presence of spatially distinct microbial communities at various depths of SSFs, suggesting the removal of specific compounds in distinct sand layers. Moreover, the persistence of a core prokaryotic community across different SSFs, SCM maturation stages, and even after disturbances like scraping, demonstrates that the biology in SSFs is resilient and likely ensures reliable SSF performance. It also implies possibilities for earlier SSF operational restart after cleaning than is conventionally done, but with continuous monitoring of water quality parameters to ensure microbial safety. These findings lay the groundwork for future research to focus on these microorganisms and their functional potential.

Integrative omics analysis reveals insights into small colony variants of Staphylococcus aureus induced by sulfamethoxazole-trimethoprim

BACKGROUND

Long-term treatment with trimethoprim-sulfamethoxazole (SXT) can lead to the formation of small-colony variants (SCVs) of Staphylococcus aureus. However, the mechanism behind SCVs formation remains poorly understood. In this study, we explored the phenotype and omics-based characterization of S. aureus SCVs induced by SXT and shed light on the potential causes of SCV formation.

METHODS

Stable SCVs were obtained by continuously treating S. aureus isolates using 12/238 µg/ml of SXT, characterized by growth kinetics, antibiotic susceptibility testing, and auxotrophism test. Subsequently, a pair of representative strains (SCV and its parental strain) were selected for genomic, transcriptomic and metabolomic analysis.

RESULTS

Three stable S. aureus SCVs were successfully screened and proven to be homologous to their corresponding parental strains. Phenotypic tests showed that all SCVs were non-classical mechanisms associated with impaired utilization of menadione, heme and thymine, and exhibited slower growth and higher antibiotic minimum inhibitory concentrations (MICs), compared to their corresponding parental strains. Genomic data revealed 15 missense mutations in 13 genes in the representative SCV, which were involved in adhesion, intramolecular phosphate transfer on ribose, transport pathways, and phage-encoded proteins. The combination analysis of transcriptome and metabolome identified 35 overlapping pathways possible associated with the phenotype switching of S. aureus. These pathways mainly included changes in metabolism, such as purine metabolism, pyruvate metabolism, amino acid metabolism, and ABC transporters, which could play a crucial role in promoting SCVs development by affecting nucleic acid synthesis and energy metabolism in bacteria.

CONCLUSION

This study provides profound insights into the causes of S. aureus SCV formation induced by SXT. The findings may offer valuable clues for developing new strategies to combat S. aureus SCV infections.

Gut-Microbiota Dysbiosis in Stroke-Prone Spontaneously Hypertensive Rats with Diet-Induced Steatohepatitis

Metabolic-dysfunction-associated fatty-liver disease (MAFLD) is the principal worldwide cause of liver disease. Individuals with nonalcoholic steatohepatitis (NASH) have a higher prevalence of small-intestinal bacterial overgrowth (SIBO). We examined gut-microbiota isolated from 12-week-old stroke-prone spontaneously hypertensive-5 rats (SHRSP5) fed on a normal diet (ND) or a high-fat- and high-cholesterol-containing diet (HFCD) and clarified the differences between their gut-microbiota. We observed that the Firmicute/Bacteroidetes (F/B) ratio in both the small intestines and the feces of the SHRSP5 rats fed HFCD increased compared to that of the SHRSP5 rats fed ND. Notably, the quantities of the 16S rRNA genes in small intestines of the SHRSP5 rats fed HFCD were significantly lower than those of the SHRSP5 rats fed ND. As in SIBO syndrome, the SHRSP5 rats fed HFCD presented with diarrhea and body-weight loss with abnormal types of bacteria in the small intestine, although the number of bacteria in the small intestine did not increase. The microbiota of the feces in the SHRSP5 rats fed HFCD was different from those in the SHRP5 rats fed ND. In conclusion, there is an association between MAFLD and gut-microbiota alteration. Gut-microbiota alteration may be a therapeutic target for MAFLD.