Bacterial genomes recovered from litter's metagenomes in Amazonian Dark Earths.

Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).

Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: a resource for fungal biology and biotechnology.

Agaricus subrufescens, also known as the "sun mushroom," has significant nutritional and medicinal value. However, its short shelf life due to the browning process results in post-harvest losses unless it's quickly dehydrated. This restricts its availability to consumers in the form of capsules.

RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing.

Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis.

Association between Dysbiosis in the Gut Microbiota of Primary Osteoporosis Patients and Bone Loss.

In recent decades, gut microbiome research has experienced significant growth, driven by technological advances that enable quantifying bacterial taxa with greater precision. Age, diet, and living environment have emerged as three key factors influencing gut microbes. Dysbiosis, resulting from alterations in these factors, may lead to changes in bacterial metabolites that regulate pro- and anti-inflammatory processes and consequently impact bone health.

The microbiome shifts throughout the gastrointestinal tract of Bradford cattle in the Pampa biome.

A deep understanding of the cattle gastrointestinal microbiome is crucial to selective breeding high-efficiency animals that produce more and generate less environmental damage. Here we performed the taxonomic identification of Bacterial and Archaeal communities using high throughput 16SrRNA gene sequencing from critical compartments of the gastrointestinal tract of Bradford cattle raised in a natural grassland in the Pampa biome, Brazil. We analyzed 110 samples, including saliva, ruminal fluid, and feces from 36 months old Bradford heifers (weighing on average 343 ± 30 kg by the sampling time).

Are the Bacteria and Their Metabolites Contributing for Gut Inflammation on GSD-Ia Patients?

Recently, patients with glycogen storage disease (GSD) have been described as having gut dysbiosis, lower fecal pH, and an imbalance in SCFAs due to an increase in acetate and propionate levels. Here, we report the fecal measurement of bacterial-related metabolites formic, acetic, lactic, propionic, and succinic acid, a key metabolite of both host and microbiota, on a previously described cohort of 24 patients (GSD Ia = 15, GSD Ib = 5, 1 GSD III = 1 and GSD IX = 3) and 16 healthy controls, with similar sex and age, using the high-performance liquid chromatography technique. The succinic acid levels were higher in the GSD patients than in the controls (patients = 38.

Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914.

Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes.

Insights into the structure and role of seed-borne bacteriome during maize germination.

Seed germination events modulate microbial community composition, which ultimately influences seed-to-seedling growth performance. Here, we evaluate the germinated maize (variety SHS 5050) root bacterial community of disinfected seed (DS) and non-disinfected seed (NDS). Using a gnotobiotic system, sodium hypochlorite (1.

Altered bacteria community dominance reduces tolerance to resident fungus and seed to seedling growth performance in maize (Zea mays L. var. DKB 177).

Seeds are reservoirs of beneficial and harmful microorganism that modulates plant growth and health. Here, we access seed to seedling bacteriome assembly modified by seed-disinfection and the underlined effect over maize germination performance and root-seedlings microbial colonization. Seed-disinfection was performed with sodium hypochlorite (1.

Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants.

Unlabelled: The purpose was identify an association between meconium microbiome, extra-uterine growth restriction, and head circumference catch-up.

Materials And Methods: Prospective study with preterm infants born <33 weeks gestational age (GA), admitted at Neonatal Unit and attending the Follow-Up Preterm Program of a tertiary hospital. Excluded out born infants; presence of congenital malformations or genetic syndromes; congenital infections; HIV-positive mothers; and newborns whose parents or legal guardians did not authorize participation.

Environmental contamination alters the intestinal microbial community of the livebearer killifish .

Intestinal microbiota perform important functions for the health of fishes. Knowing the microbial composition and evaluating the possible effects caused by anthropogenic pollution in the intestinal microbiota of fish populations might represent an important step in defining microbial biomarkers for water pollution. This study evaluated the impact of environmental contamination on the gut microbiota of the livebearer killifish .

Microbial patterns in rumen are associated with gain of weight in beef cattle.

Ruminal microorganisms play a pivotal role in cattle nutrition. The discovery of the main microbes or of a microbial community responsible for enhancing the gain of weight in beef cattle might be used in therapeutic approaches to increase animal performance and cause less environmental damages. Here, we examined the differences in bacterial and fungal composition of rumen samples of Braford heifers raised in natural grassland of the Pampa Biome in Brazil.

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn's gut colonization.

The female lower genital tract harbors a complex microbial community essential for homeostasis and health. During pregnancy, the female body undergoes unique hormonal changes that contribute to weight gain as well as modulations in immune function that can affect microbiota composition. Several studies have described the vaginal microbiota of pregnant women from the USA, Europe and Mexico.

Defining microbial biomarkers for risk of preterm labor.

Preterm birth remains the main contributor to early childhood mortality. The vaginal environment, including microbiota composition, might contribute to the risk of preterm delivery. Alterations in the vaginal microbial community structure might represent a risk factor for preterm birth.

Correction: Hepatic glycogen storage diseases are associated to microbial dysbiosis.

[This corrects the article DOI: 10.1371/journal.pone.

High-throughput sequencing analysis of insights into repetitive DNA, gene content and potential biotechnological applications.

In this study, the Ion Torrent PGM platform was employed to conduct a whole-genome sequencing analysis of L., aiming to generate new genomic information for this non-model species. The whole-genome set of assembled sequences (WGSAS) generated 2601 contigs, with a cumulative length of 3.

Hepatic glycogen storage diseases are associated to microbial dysbiosis.

Introduction: The gut microbiome has been related to several features present in Glycogen Storage Diseases (GSD) patients including obesity, inflammatory bowel disease (IBD) and liver disease.

Objectives: The primary objective of this study was to investigate associations between GSD and the gut microbiota.

Methods: Twenty-four GSD patients on treatment with uncooked cornstarch (UCCS), and 16 healthy controls had their faecal microbiota evaluated through 16S rRNA gene sequencing.

Characterization of Plastidial and Nuclear SSR Markers for Understanding Invasion Histories and Genetic Diversity of L.

Invasive plant species are expected to display high dispersal capacity but low levels of genetic diversity due to the founder effect occurring at each invasion episode. Understanding the history of invasions and the levels of genetic diversity of such species is an important task for planning management and monitoring strategy for these events. Peruvian Peppertree ( L.

Do probiotics effectively ameliorate glycemic control during gestational diabetes? A systematic review.

Background: Gestational diabetes mellitus (GDM) is defined as any degree of glucose intolerance with onset or first recognition during pregnancy. The aim of this work was to systematically review all studies in which probiotic supplements were used during pregnancy and analyse the effects on GDM.

Methods: The data were collected using the medical subheading (MeSH) terms: ("diabetes, gestational"[MeSH Terms] OR ("diabetes"[All Fields] AND "gestational"[All Fields]) OR "gestational diabetes"[All Fields] OR ("gestational"[All Fields] AND "diabetes"[All Fields])) AND ("probiotics"[MeSH Terms] OR "probiotics"[All Fields]).

Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and NO emissions.

Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (NO) emissions.

Differences in bacterial composition between men's and women's restrooms and other common areas within a public building.

Humans distribute a wide range of microorganisms around building interiors, and some of these are potentially pathogenic. Recent research established that humans are the main drivers of the indoor microbiome and up to now significant literature has been produced about this topic. Here we analyzed differences in bacterial composition between men's and women's restrooms and other common areas within the same public building.