Human microbiota is a complex consortium of microorganisms involved in the proper functioning of almost every system of the organism. Majority of the human diseases are associated with the development of intestinal dysbiosis. Dysbiotic condition or dysbiosis is a key pathogenic condition causing many severe infectious or non-infectious diseases. Rapid return to the original microbiota in many cases leads to the fast recovery from the disease. However, the optimal way of the treatment of dysbiosis is still under the discussion. Recently we have developed a method of autoprobiotics based on using isolated indigenous bacteria for improving of microbiota condition. The method based on feeding the patients with bacterial products grown from their personal, genetically characterised strains have been successfully tested in clinic on patients with IBS or chronic pneumonia. In present study we tried to evaluate technology employing autoprobiotic bacteria belonging to different species employing the rat model of antibiotic induced dysbiosis. Six experimental groups of animals after taking antibiotics were treated with different variants of autoprobiotics (lactobacillus, bifidobacteria, enterococcus, their mixture, fecal microbiota, or anaerobically grown complex of indigenous microbiota) prepared for each of them before the development of dysbiosis. Judging by the multiple parameters including metagenomics analysis of microbiota, immune status and microbiota content of the animals with dysbiosis relatively to control group, the most pronounced positive changes were provided by autoprobiotics based on enterococci, bifidobacteria or the consortium of indigenous bacteria grown under anaerobic conditions. These groups of autoprobiotics were delivering the most effective restoration of the original microbiota content and significant anti-inflammatory reaction of the immune system.

Background: Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at the 3′ ends within the overlapping region prevents the accurate combining of significant portion of read pairs. Recently CD-HIT-OTU-Miseq was presented as a new approach for 16S analysis using the paired-end reads, it completely avoids the reads merging process due to separate clustering of paired reads. CD-HIT-OTU-Miseq is a set of tools which are supposed to be successively launched by auxiliary shell scripts. This launch mode is not suitable for processing of big amounts of data generated in modern omics experiments. To solve this issue we created CDSnake – Snakemake pipeline utilizing CD-HIT tools for easier consecutive launch of CD-HIT-OTU-Miseq tools for complete processing of paired end reads in metagenomic studies. Usage of pipeline make 16S analysis easier due to one-command launch and helps to yield reproducible results. Results: We benchmarked our pipeline against two commonly used pipelines for OTU retrieval, incorporated into popular workflow for microbiome analysis, QIIME2 - DADA2 and deblur. Three mock datasets having highly overlapping paired-end 2 × 250 bp reads were used for benchmarking - Balanced, HMP, and Extreme. CDSnake outputted less OTUs than DADA2 and deblur. However, on Balanced and HMP datasets number of OTUs outputted by CDSnake was closer to real number of strains which were used for mock community generation, than those outputted by DADA2 and deblur. Though generally slower than other pipelines, CDSnake outputted higher total counts, preserving more information from raw data. Inheriting this properties from original CD-HIT-OTU-MiSeq utilities, CDSnake made their usage handier due to simple scalability, easier automated runs and other Snakemake benefits. Conclusions: We developed Snakemake pipeline for OTU-MiSeq utilities, which simplified and automated data analysis. Benchmarking showed that this approach is capable to outperform popular tools in certain conditions.

An amendment to this paper has been published and can be accessed via the original article.