Biology subjects

Busi, S. B.

Publications and source records attributed to Busi, S. B..

4 recordsLinked to original sources

bioRxiv2021

Synergistic effect of short- and long-read sequencing on functional meta-omics

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only, and hybrid assembly approaches on four different metagenomic samples of varying complexity and demonstrate how they affect gene and protein inference which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions and we propose a reference-independent solution based on the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.

microbiology↗

bioRxiv2020

Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome

Microdiversity, the organization of microorganisms into groups with closely related but ecologically different sub-types, is widespread and represents an important linchpin between microbial ecology and evolution. However, the drivers of microdiversification remain largely unknown. Here we show that selection promotes microdiversity in the microbiome associated with sediments in glacier-fed streams (GFS). Applying a novel phylogenetic framework, we identify several clades that are under homogeneous selection and that contain genera with higher levels of microdiversity than the rest of the genera. Overall these clades constituted [~]44% and [~]64% of community -diversity and abundance, and both percentages increased further in GFS that were largely devoid of primary producers. Our findings show that strong homogeneous selection drives the microdiversification of specialized microbial groups putatively underlying their success in the extreme environment of GFS. This microdiversity could be threatened as glaciers shrink, with unknown consequences for microbial diversity and functionality in these ecosystems.

ecology↗

bioRxiv2020

Integrated metabolome and transcriptome analyses provide insight into colon cancer development by the gut microbiota

Colon cancer onset and progression is strongly associated with the presence, absence, or differences in relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex commensal bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development in a preclinical rat model of colon cancer. Fecal samples from rats harboring distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We collected samples prior to observable disease onset and identified putative metabolite profiles that predicted future disease severity, independent of GM status. Transcriptome analyses performed after disease onset from normal epithelium and tumor tissues between the high and low tumor GMs suggests that the GM is correlated with altered host gene expression. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344) along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to reveal signatures of susceptibility and resistance and integrated analyses to reveal common pathways that are likely to be universal targets for intervention. Statement of significanceFecal metabolites, influenced by the gut microbiota, correlate with colon adenoma risk in a preclinical model of familial colon cancer.

cancer biology↗

bioRxiv2020

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecology, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a "mock" community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.

molecular biology↗