Metagenomic Exploration of Koumiss from Kazakhstan.
Ontology highlight
ABSTRACT:
SUBMITTER: Bogoyavlenskiy A
PROVIDER: S-EPMC8759390 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Here, we report the metagenomic analysis of the gut of Atelerix albiventris, an animal typically kept as a pet in Kazakhstan. In this case, shotgun metagenomic sequencing of the RNA and DNA viral community was performed.
| S-EPMC8407749 | biostudies-literature
Project description:BACKGROUND:Koumiss is a naturally fermented mare's milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. RESULTS:A total of 119 bacterial and 36 yeast species were identified among the 14 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactococcus raffinolactis, and Citrobacter freundii. The main yeast species were Dekkera anomala, Kazachstania unispora, Meyerozyma caribbica, Pichia sp.BZ159, Kluyveromyces marxianus, and uncultured Guehomyces. The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora, Dekkera anomala, and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami. CONCLUSIONS:Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast species and taste also were found.
| S-EPMC7149844 | biostudies-literature
Project description:The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction (<0.1 µm). Phylogenetic approaches were also used to identify predicted proteins of viral origin in the larger fractions of data from all Indian Ocean samples, which were included in subsequent metagenomic analyses. Taxonomic profiling of viral sequences suggested that size fractionation of marine microbial communities enriches for specific groups of viruses within the different size classes and functional characterization further substantiated this observation. Functional analyses also revealed a relative enrichment for metabolic proteins of viral origin that potentially reflect the physiological condition of host cells in the Indian Ocean including those involved in nitrogen metabolism and oxidative phosphorylation. A novel classification method, MGTAXA, was used to assess virus-host relationships in the Indian Ocean by predicting the taxonomy of putative host genera, with Prochlorococcus, Acanthochlois and members of the SAR86 cluster comprising the most abundant predictions. This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions.
| S-EPMC3474794 | biostudies-literature
Project description:Viruses are the most abundant biological entities on Earth and can be found in a variety of environments. A high prevalence of viruses in marine and freshwater systems was initially reported by Spencer in 1955, but the ecological significance of viruses is insufficiently known even until the present day. Viruses are known to play a key role in the biology of freshwater bacteria: controlling the bacterial abundance, composition of species, and acting as intermediaries in the transfer of genes between bacterial populations. In our study a variety of viromes of the Ile-Balkhash water basin were identified. It was found that the composition of viruses of the Ile-Balkhash region is made up not only of a wide variety of autochthonous viruses typical for phytoplankton hydro ecosystems, but also of representatives of allochthonous viruses-such families as Coronaviridae, Reoviridae and Herpesviridae-indicating anthropogenic pollution of the basin. The research designed to investigate the viral abundance, spread, infectious cycle, seasonal dynamics, composition of the viral community, and the influence of viruses on the bacteria, phytoplankton and recycling of nutrients, as well as the impact of environmental factors on the viral ecology in a variety of marine and freshwater systems is very relevant nowadays.
| S-EPMC5377873 | biostudies-other
Project description:This is a pioneering report on the metagenomic exploration of the bacterial diversity from a busy sea port in Paradip, Odisha, India. In our study, high-throughput sequencing of community 16S rRNA gene amplicon was performed using 454 GS Junior platform. Metagenome contain 34,121 sequences with 16,677,333 bp and 56.3% G + C content. Metagenome sequences data are now available at NCBI under the Sequence Read Archive (SRA) database with accession no. SRX897055. Community metagenome sequence revealed the presence of 11,705 species belonging to 40 different phyla. Bacteroidetes (23%), Firmicutes (19%), Proteobacteria (17%), Spirochaetes (10%), Nitrospirae (8%), Actinobacteria (7%) and Acidobacteria (3%) are the predominant bacterial phyla in this port soil. Analysis of metagenomic sequences unfolded the interesting distribution of several phyla which pointed to the significant anthropogenic intervention influencing the bacterial community character of this port.
| S-EPMC4778619 | biostudies-literature
Project description:Mine tailings from copper mines are considered as one of the sources of highly hazardous acid mine drainage (AMD) due to bio-oxidation of its sulfidic constituents. This study was designed to understand microbial community composition and potential for acid generation using samples from mine tailings of Malanjkhand copper project (MCP), India through 16S rRNA gene based amplicon sequencing approach (targeting V4 region). Three tailings samples (T1, T2 and T3) with varied physiochemical properties selected for the study revealed distinct microbial assemblages. Sample (T3) with most extreme nature (pH < 2.0) harbored Proteobacteria, Actinobacteria, Chloroflexi while the samples (T1 and T3) with slightly moderate nature (pH < 4.0 and > 3.0) exhibited abundance of Proteobacteria, Fimicutes, Actinobacteria and/or Nitrospirae. Metagenomic sequences are available under the BioProject ID PRJNA361456.
| S-EPMC5315440 | biostudies-literature
Project description:BackgroundElucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity.ResultsHere, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids.ConclusionsOverall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.
| S-EPMC6712665 | biostudies-literature
Project description:Koumiss is a fermented mare's milk beverage that has attracted increasing attention due to its nutritional richness and important economic value. Bacteria in koumiss play a major role in pH decreasing and reducing spoilage through bacterial inhibition. The dynamic changes in nutritional content were determined firstly during fermentation, and then the metagenomics sequencing technology was applied to profile koumiss core microbiota at the species level. We also clarified the function and effect of the bacteria on the nutritional content of the final product. We also investigated active microbial function by comparing the metagenomics of representative samples collected at different time points during the fermentation process. This study dynamically revealed the bacterial composition and function of traditional koumiss during its making process. Twenty-three major functional categories related to amino acid and fat synthesis, metabolism, and so on were identified. Functional category L (represented replication-, recombination-, and repair-related functions) was one of the most important categories with the highest relative abundance in all of the 23 major functional categories. CoG category having a significant correlation with Lactococcus piscium was the most abundant. The change in metabolic activity of bacteria at different fermentation time points showed that the metabolic activity was more active in the first 24 hr and then began to stabilize. LAB play the major role in the koumiss pH decreasing and quality improvement. The functional genes of related metabolic activity of lactic acid bacteria were more active in the first 24 hr of koumiss fermentation and then began to stabilize.
| S-EPMC8358363 | biostudies-literature
Project description:The detection and characterization of emerging infectious agents has been a continuing public health concern. High Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies have proven to be promising approaches for efficient and unbiased detection of pathogens in complex biological samples, providing access to comprehensive analyses. As NGS approaches typically yield millions of putatively representative reads per sample, efficient data management and visualization resources have become mandatory. Most usually, those resources are implemented through a dedicated Laboratory Information Management System (LIMS), solely to provide perspective regarding the available information. We developed an easily deployable web-interface, facilitating management and bioinformatics analysis of metagenomics data-samples. It was engineered to run associated and dedicated Galaxy workflows for the detection and eventually classification of pathogens. The web application allows easy interaction with existing Galaxy metagenomic workflows, facilitates the organization, exploration and aggregation of the most relevant sample-specific sequences among millions of genomic sequences, allowing them to determine their relative abundance, and associate them to the most closely related organism or pathogen. The user-friendly Django-Based interface, associates the users' input data and its metadata through a bio-IT provided set of resources (a Galaxy instance, and both sufficient storage and grid computing power). Galaxy is used to handle and analyze the user's input data from loading, indexing, mapping, assembly and DB-searches. Interaction between our application and Galaxy is ensured by the BioBlend library, which gives API-based access to Galaxy's main features. Metadata about samples, runs, as well as the workflow results are stored in the LIMS. For metagenomic classification and exploration purposes, we show, as a proof of concept, that integration of intuitive exploratory tools, like Krona for representation of taxonomic classification, can be achieved very easily. In the trend of Galaxy, the interface enables the sharing of scientific results to fellow team members.
| S-EPMC5405795 | biostudies-literature
Project description:Lactobacillus sp. Koumiss Genome sequencing
| PRJNA445914 | ENA