Gut biome

Mental health conditions have been linked closely to an imbalance of microbiota in the gut, leading to disruption of the microbiome (dysbiosis). Several neurotransmitters, such as GABA (gamma-aminobutyric acid), serotonin, and glutamate, are produced in the gut, which are associated with anxiety and depressive symptoms. Mental health and the gut have been linked closely, and many mental illnesses have been associated with gut dysbiosis. Probiotics are marketed to improve gut health, act as mood enhancers, and be effective in reducing stress as unregulated over-the-counter supplements...

Changes in the gut microbiome cause recolonization by pathogens and inflammatory responses, leading to the development of intestinal disorders. Probiotics administration has been proposed for many years to reverse the intestinal dysbiosis and to enhance intestinal health. This study aimed to evaluate the inhibitory effects of two newly designed probiotic mixtures, Consti-Biome and SensiBiome, on two enteric pathogens Staphylococcus aureus and Escherichia coli that may cause intestinal disorders. Additionally, the study was designed to evaluate whether Consti-Biome and Sensi-Biome could modulate the immune response, produce short-chain fatty acids (SCFAs), and reduce gas production...

BACKGROUND: Human life quality and expectancy have increased dramatically over the past 5 decades because of improvements in nutrition and antibiotic's usage fighting against infectious diseases. Yet, it was soon revealed that the microbes adapted to develop resistance to any of the drugs that were used. Recently, there is great concern that commensal bacteria from food and the gastrointestinal tract of humans and animals could act as a reservoir for antibiotic resistance genes. Methodology ...

The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction...

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Olea europaea subsp . africana (Mill.) P.S. Green (medium-sized tree species known as "African wild olive"), provides important ecological goods and services for sustaining frugivores in the grassland biome in South Africa. We speculate that O. europaea subsp. africana's population has been declining due to habitat loss and exploitation for domestic benefits suggesting an unrecognized conservation threat. Therefore, the study aimed to investigate the anthropogenic conservation threats for O. europaea subsp ...

BACKGROUND: Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity. OBJECTIVE: Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes...

As an omnipresent opportunistic bacterium, Pseudomonas aeruginosa PAO1 is responsible for acute and chronic infection in immunocompromised individuals. Currently, this bacterium is on WHO's red list where new antibiotics are urgently required for the treatment. Finding essential genes and essential hypothetical proteins (EHP) can be crucial in identifying novel druggable targets and therapeutics. This study is aimed at characterizing these EHPs and analyzing subcellular and physiochemical properties, PPI network, nonhomologous analysis against humans, virulence factor and novel drug target prediction, and finally structural analysis of the identified target employing around 42 robust bioinformatics tools/databases, the output of which was evaluated using the ROC analysis...

Sixteen yeast isolates representing two novel species of the genus Sugiyamaella were obtained from passalid beetles, their galleries and rotting wood collected in three sites of Amazonian Forest in Brazil. Sequence analyses of the ITS-5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the first species, described here as Sugiyamaella amazoniana f. a., sp. nov. (holotype CBS 18112, MycoBank 847461) is phylogenetically related to S. bonitensis with these species differing by 37 nucleotide substitutions and six gaps in D1/D2 sequences...

The common antibiotic oxytetracycline (OTC) is nowadays commonly found in natural aquatic environments. However, the underlying mechanisms of low-dose OTC exposure and its neurotoxic effects on aquatic animals remain unknown. In this study, we exposed zebrafish larvae to environmental concentrations of OTC in early life and performed neurobehavioral, 16S rRNA gene sequencing, and transcriptomic analyses. OTC exposure resulted in hyperactivity of larvae and a significant reduction in the number of neurons in the midbrain...

Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil)...

The Dirichlet-multinomial (DM) distribution plays a fundamental role in modern statistical methodology development and application. Recently, the DM distribution and its variants have been used extensively to model multivariate count data generated by high-throughput sequencing technology in omics research due to its ability to accommodate the compositional structure of the data as well as overdispersion. A major limitation of the DM distribution is that it is unable to handle excess zeros typically found in practice which may bias inference...

Huoxiang Zhengqi Oral Liquid (HZOL) is a classic Chinese patent medicine used in China for more than 1,000 years in treating gastrointestinal and respiratory diseases. Clinically applied HZOL in early respiratory disease stages can reduce the proportion of lung infection patients that progress to severe acute lung injury (ALI). However, few pharmacological studies evaluated its level of protection against ALI. We explored mechanisms of HZOL against ALI by employing network pharmacology, molecular docking, and rat experiments...

The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment...

Differences in the bacterial communities inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analyzed the gut microbiomes of 14 sympatric small-mammal species in a semi-arid African savanna, hypothesizing that there would be a strong phylosymbiotic pattern associated with differences in their body sizes and diets...

Little knowledge is available in literature regarding the chemical composition and health-promoting effects of baru (Dipteryx alata Vog.) pulp, a by-product usually discarded by the agro-industry during the processing of baru fruit. This study evaluated the chemical composition of baru pulp and investigated its prebiotic activity on distinct probiotic strains and human colonic microbiota with in vitro assays. Baru pulp had high contents of insoluble dietary fibers and phenolic compounds (mainly hesperidin)...

BACKGROUND: The study of the ecology of Trypanosoma cruzi is challenging due to its extreme adaptive plasticity, resulting in the parasitism of hundreds of mammal species and dozens of triatomine species. The genetic analysis of blood meal sources (BMS) from the triatomine vector is an accurate and practical approach for gathering information on which wild mammal species participate in a local transmission network. South American coatis, Nasua nasua, act as important reservoir host species of T...

IgA-coated bacteria in the gut (IgA-biome) provide a homeostatic function in healthy people through inhibition of microbial invaders and by protecting the epithelial monolayer of the gut. The laboratory methods used to detect this group of bacteria require flow cytometry and DNA sequencing (IgA-Seq). With dysbiosis (reduced diversity of the microbiome), the IgA-biome also is impaired. In the presence of enteric infection, oral vaccines, or an intestinal inflammatory disorder, the IgA-biome focuses on the pathogenic bacteria or foreign antigens, while in other chronic diseases associated with dysbiosis, the IgA-biome is reduced in capacity...

For decades, the potential role of probiotics in the prevention and treatment of recurrent urinary tract infections has been extensively studied. However, achieving an effective problem-solving strategy has thus far proven elusive. Perhaps adopting a military paradigm might expedite our assault on chronic, recurring bacteriuria in women. What is needed is a targeted strategy with specific attention to (1) the enemy: the case-specific uropathogen; (2) the battlefield: the extraordinarily complex interplay of factors within the bladder, unique to a given patient, which interface with profoundly important influences from the gut biome, as well as the vaginal biota; (3) the weapon: an antimicrobial probiotic with demonstrated activity against that specific uropathogen; (4) a new strategy: taking these complexities into account, we posit a key role for the instillation of case-specific lactobacilli directly into the bladder of the designated patient...

BACKGROUND AND OBJECTIVE: The gut microbiota (GM) was recently recognized to play an important role in modulating systemic immune responses and is known to influence the effects or adverse events of immune checkpoint blockade (ICB) or carcinogenesis by crosstalk with regulators of cancer-related immunity, and this relationship is complex and multifactorial. Diversity in the gut microbiome and the abundance of specific bacterial species have been identified to be associated with better response and prognosis...