Biology subjects

Anslan, S.

Publications and source records attributed to Anslan, S..

3 recordsLinked to original sources

bioRxiv2019

Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods

Sample type and preservation methods are likely to influence microbiome analysis results. Relatively few studies have explored the differences between feces and gut as well as ethanol-stored and frozen samples. Here, we sampled the same individuals of three aquatic vertebrates from the Qinghai-Tibetan Plateau non-invasively for feces, and subsequently for hindgut through dissection. Our study species, two fishes (Gymnocypris cf. namensis and Triplophysa sp.) and one amphibian (tadpoles of Nanorana parkeri), were all collected at the same time and site. Gut and fecal samples were stored in ethanol, and additionally, part of the gut samples were frozen, but temporarily thawed during transport as it often happens under difficult field conditions. Our results showed that both substrate (gut content vs. feces) as well as preservation method can influence the analysis of intestinal microbiomes. Frozen gut samples strongly differed from ethanol-stored samples, and especially in Nanorana most frozen samples were dominated (in relative abundance) by a set of Proteobacteria OTUs that were completely absent from the ethanol-stored samples. This blooming of contaminant bacteria occurred after less than 12 h of thawing, thus caution should be taken when constancy of cold temperatures cannot be maintained in the field for sample preservation purposes. Among ethanol-stored samples, bacterial communities from feces differed from those recovered from guts, but in part recovered similar patterns, such as a higher bacterial richness in the more herbivorous Nanorana tadpoles. Although our results argue against combining gut and fecal samples in analyses of host-specific microbiome differences, they also confirm that non-invasive sampling of feces can provide useful information of gut microbiomes in aquatic vertebrates, which may be important especially when working with endangered species.

microbiology↗

bioRxiv2019

Comparative genomic analysis reveals a monophyletic cold adapted Arthrobacter cluster from polar and alpine regions

Decrease in the frequency of arginine and increase in lysine are the trends that have been identified in the genomes of cold adapted bacteria. However, some cold adapted taxa show only limited or no detectable changes in the frequencies of amino acid composition. Here, we examined Arthrobacter spp. genomes from a wide range of environments on whether the genomic adaptations can be conclusively identified across genomes of taxa from polar and alpine regions. Phylogenetic analysis with a concatenated alignment of 119 orthologous proteins revealed a monophyletic clustering of seven polar and alpine isolated strains. Significant changes in amino acid composition related to cold adaptation were exclusive to seven of the twenty-nine strains from polar and alpine regions. Analysis of significant indicator genes and cold shock genes also revealed that clear differences could only be detected in the same seven strains. These unique characteristics may result from a vast exchange of genome content at the node leading to the monophyletic cold adapted Arthrobacter cluster predicted by the birth-and-death model. We then experimentally validated that strains with significant changes in amino acid composition have a better capacity to grow at low temperature than the mesophilic strains.\n\nImportanceAcquisition of novel traits through horizontal gene transfer at the early divergence of the monophyletic cluster may accelerate their adaptation to low temperature. Our study reached a clear relationship between adaptation to cold and genomic features and would advanced in understanding the ambiguous results produced by the previous studies on genomic adaption to cold temperature.

microbiology↗

bioRxiv2019

Relative performance of Oxford Nanopore MinION vs. Pacific Biosciences Sequel third-generation sequencing platforms in identification of agricultural and forest pathogens

Culture-based molecular characterization methods have revolutionized detection of pathogens, yet these methods are either slow or imprecise. The second-generation sequencing tools have much improved precision and sensitivity of detection, but the analysis processes are costly and take several days. Of third-generation techniques, the portable Oxford Nanopore MinION device has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performance of two third-generation sequencing instruments, MinION and Pacific Biosciences Sequel in identification and diagnostics of pathogens from conifer needles and potato leaves and tubers. We demonstrate that Sequel is efficient in metabarcoding of complex samples, whereas MinION is not suited for this purpose due to the high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms from plant tissues following both amplicon-based and metagenomics-based approaches. Using the PCR-free approach with shortened extraction and incubation times, we performed the entire MinION workflow from sample preparation through DNA extraction, sequencing, bioinformatics and interpretation in two and half hours. We advocate the use of MinION for rapid diagnostics of pathogens, but care needs to be taken to control or account for all potential technical biases.\n\nIMPORTANCEWe develop new and rapid protocols for MinION-based third-generation diagnostics of plant pathogens that greatly improves the speed and precision of diagnostics. Due to high error rate and technical biases in MinION, PacBio Sequel platform is more useful for amplicon-based metabarcoding from complex biological samples.

microbiology↗