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Scientific Reports Apr 2023Gut microbiota is established to be associated with the diversity of gastrointestinal conditions, but information on the variation associated with music and gut microbes...
Gut microbiota is established to be associated with the diversity of gastrointestinal conditions, but information on the variation associated with music and gut microbes is limited. Current study revealed the impacts of music intervention during feeding on the growth performance and gut microbes of mice by using clinical symptoms and 16S rRNA sequencing techniques. The results showed that feeding mice with music had a significant increase in body weight after the 25th day. The Firmicutes and Proteobacteria were the most dominant phylum in the gut microbiota. Also, the relative abundance of the dominant bacteria was variable after musical intervention. In contrast to the control group, a significant decrease in alpha diversity analysis of gut bacterial microorganisms and Metastats analysis showed a significant increase in the relative abundance of 5 genera and one phylum after the music intervention. Moreover, the musical intervention during feeding caused modifications in the gut microbial composition of mice, as evidenced by an increase in the level of Firmicutes and Lactobacillus, while decreases the richness of pathogenic bacteria, e.g. Proteobacteria, Cyanobacteria and Muribaculaceae, etc. In summary, music intervention increased body weight and enhanced the abundance of beneficial bacteria by reducing the prevalence of pathogenic bacteria in gut microbiota of mice.
Topics: Animals; Mice; Gastrointestinal Microbiome; Music; RNA, Ribosomal, 16S; Proteobacteria; Firmicutes; Cyanobacteria; Body Weight
PubMed: 37072501
DOI: 10.1038/s41598-023-33522-3 -
The Science of the Total Environment Feb 2023Brackish water aquaculture has brought numerous economic benefits, whereas anthropogenic activities in aquaculture may cause the dissemination of antibiotic resistance...
Brackish water aquaculture has brought numerous economic benefits, whereas anthropogenic activities in aquaculture may cause the dissemination of antibiotic resistance genes (ARGs) in brackish water sediments. The intricate relationships between environmental factors and microbial communities as well as their role in ARGs dissemination in brackish water aquaculture remain unclear. This study applied PCR and 16S sequencing to identify the variations in ARGs, class 1 integron gene (intI1) and microbial communities in brackish water aquaculture sediment. The distribution of ARGs in brackish water aquaculture sediment was similar to that in freshwater aquaculture, and the sulfonamide resistance gene sul1 was the indicator of ARGs. Proteobacteria and Firmicutes were the dominant phyla, and Paenisporosarcina (p_ Firmicutes) was the dominant genus. The results of correlation, network and redundancy analysis indicated that the microbial community in the brackish water aquaculture sediment was function-driven. The neutral model and variation partitioning analysis were used to verify the ecological processes of the bacterial community. The normalized stochasticity ratio showed that pond bacteria community was dominated by determinacy, which was affected by aquaculture activities. The total nitrogen and organic matter influenced the abundance of ARGs, while Proteobacteria and Thiobacillus (p_Proteobacteria) were the key antibiotic-resistant hosts. Our study provides insight into the prevalence of ARGs in brackish water aquaculture sediments, and indicates that brackish water aquaculture is a reservoir of ARGs.
Topics: Genes, Bacterial; Anti-Bacterial Agents; Drug Resistance, Microbial; Bacteria; Aquaculture; Proteobacteria; Saline Waters; China
PubMed: 36436623
DOI: 10.1016/j.scitotenv.2022.160475 -
Scientific Reports Jan 2024In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal...
In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO), phosphate (P), ammonia (NH), and nitrate (NO) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.
Topics: RNA, Ribosomal, 16S; Brazil; Proteobacteria; Ammonia; Water
PubMed: 38267511
DOI: 10.1038/s41598-024-52432-6 -
Environmental Microbiology Reports Jun 2020The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa...
The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.
Topics: Actinobacteria; Bacteria; Bacteroidetes; Cyanobacteria; Gulf of Mexico; Metagenomics; Microbiota; Nitrogen; Phylogeny; Planctomycetales; Plankton; Polyamines; Proteobacteria; RNA, Ribosomal, 16S; Seawater; Transcriptome
PubMed: 32227463
DOI: 10.1111/1758-2229.12841 -
Current Microbiology Jun 2022Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent...
Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
Topics: Alphaproteobacteria; Bacterial Proteins; Gammaproteobacteria; Phylogeny; Proteobacteria; RNA, Ribosomal, 16S
PubMed: 35704242
DOI: 10.1007/s00284-022-02910-9 -
Microbial Physiology 2021Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial...
Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival. We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.
Topics: Adaptation, Physiological; Animals; Bacteria; Gammaproteobacteria; Heterotrophic Processes; Proteobacteria
PubMed: 34058747
DOI: 10.1159/000516215 -
Scientific Reports Dec 2019The composition of fungal and bacterial communities in three polythermal glaciers and associated aquatic environments in Kongsfjorden, Svalbard was analysed using a...
The composition of fungal and bacterial communities in three polythermal glaciers and associated aquatic environments in Kongsfjorden, Svalbard was analysed using a combination of cultivation and amplicon sequencing. 109 fungal strains belonging to 30 mostly basidiomycetous species were isolated from glacial samples with counts up to 10 CFU/100 ml. Glaciozyma-related taxon and Phenoliferia psychrophenolica were the dominant species. Unexpectedly, amplicon sequencing uncovered sequences of Chytridiomycota in all samples and Rozellomycota in sea water, lake water, and tap water. Sequences of Malassezia restricta and of the extremely halotolerant Hortaea werneckii were also found in subglacial habitats for the first time. Overall, the fungal communities within a glacier and among glaciers were diverse and spatially heterogenous. Contrary to this, there was a large overlap between the bacterial communities of different glaciers, with Flavobacterium sp. being the most frequently isolated. In amplicon sequencing Actinobacteria and Proteobacteria sequences were the most abundant.
Topics: Bacteria; Basidiomycota; Biodiversity; Ecosystem; Fresh Water; Fungi; Genetic Variation; Geography; Ice Cover; Proteobacteria; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Species Specificity; Svalbard
PubMed: 31882659
DOI: 10.1038/s41598-019-56290-5 -
Journal of Invertebrate Pathology Nov 2021With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately... (Review)
Review
With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.
Topics: Animal Feed; Animals; Aquaculture; Diet; Dietary Supplements; Gastrointestinal Microbiome; Penaeidae; Proteobacteria
PubMed: 32330478
DOI: 10.1016/j.jip.2020.107387 -
Microbiological Research Sep 2021The symbiosis between legumes and nodulating Proteobacteria (so-called rhizobia) contributes greatly to nitrogen fixation in terrestrial ecosystems. Root nodulating...
The symbiosis between legumes and nodulating Proteobacteria (so-called rhizobia) contributes greatly to nitrogen fixation in terrestrial ecosystems. Root nodulating Proteobacteria produce nodulation (Nod) factors during the initiation of rhizobial nodule organogenesis on the roots of legumes. Here, we screened the Nod factor production capacity of the previously reported nodule inducing Proteobacteria genera using their genome sequences and assessed the evolutionary history of symbiosis based on phylogenomics. Our analysis revealed 12 genera as potentially Nod factor producing taxa exclusively from alpha- and beta-Proteobacteria. Based on molecular clock analysis, we estimate that rhizobial nitrogen-fixing symbiosis appeared for the first time about 51 Mya (Eocene epoch) in Rhizobiaceae, and it was laterally transferred to multiple symbiotic taxa in alpha- and beta-Proteobacteria. Coevolutionary tests conducted for measuring the phylogenetic congruence between hosts and symbionts revealed only weak topological similarity between legumes and their bacterial symbionts. We conclude that frequent lateral transfer of symbiotic genes, facultative symbiotic nature of rhizobia, differential evolutionary processes of chromosome versus plasmids, and complex multispecies coevolutionary processes have shaped the rhizobia-host associations.
Topics: Alphaproteobacteria; Betaproteobacteria; Ecosystem; Fabaceae; Gene Transfer, Horizontal; Mimosa; Nitrogen Fixation; Phylogeny; Plant Root Nodulation; Rhizobium; Symbiosis
PubMed: 34051611
DOI: 10.1016/j.micres.2021.126788 -
Nature Communications Dec 2019Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving...
Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, 'Candidatus Uab amorphum', which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the 'Ca. Uab amorphum' genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this "phagotrophic" bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells.
Topics: Alphaproteobacteria; Bacterial Proteins; Biological Evolution; Genome, Bacterial; Phagocytosis; Phylogeny
PubMed: 31827088
DOI: 10.1038/s41467-019-13499-2