The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy.

The maternal pregnancy microbiome (including genitourinary and gut) has been linked to important pregnancy/birth and later childhood health outcomes. However, such sampling as part of large population cohort studies is logistically and financially challenging. Many countries routinely collect vaginal or vaginal-rectal swabs in late pregnancy for Group B Streptococcus (GBS) screening, but their utility for population-based research is still unclear.

Disease-specific loss of microbial cross-feeding interactions in the human gut.

Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us to identify and rank metabolic interactions that are significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases.

Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease.

Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies.

Occlusal Changes with Clear Aligners and the Case Complexity Influence: A Longitudinal Cohort Clinical Study.

Background: Clear aligners (CA) are used 22 h daily, creating a bite-block effect. This work aims to (i) analyze occlusal changes before the beginning of treatment, after the first set of CA and after the use of additional aligners; (ii) compare planned occlusal contacts with the ones obtained after the first set of CA; (iii) analyze the occlusal changes occurred after reaching the orthodontic goals after 3 months of using CA only at night; (iv) evaluate and characterize which tooth movements did not allow the treatment to be completed at the end of the first set of aligners, and finally (v) verify the possible relation between the changes in occlusal contact and areas and parameters such as case complexity and facial biotype.

Materials And Methods: A quantitative, comparative, and observational longitudinal cohort study design was implemented to evaluate the clinical data and the complexity levels of cases receiving CA.

Extensive genome analysis identifies novel plasmid families in .

Globally, the anaerobic bacterium causes severe disease in a wide array of hosts; however, strains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources.

Masticatory Function in Individuals with Temporomandibular Disorders: A Systematic Review and Meta-Analysis.

The literature search was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol in the PubMed, Cochrane Library, LILACS, EBSCO, Scielo, between 2012 and 2022. The methodological quality was assessed by using the Newcastle-Ottawa Study Quality Assessment Scale. Mean differences and 95% confidence intervals were calculated and combined in meta-analyses.

expam-high-resolution analysis of metagenomes using distance trees.

Summary: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing.

Availability And Implementation: expam is an open-source Python application released under the GNU General Public Licence v3.

The Role of Pain Inflexibility and Acceptance among Headache and Temporomandibular Disorders Patients.

Temporomandibular disorders (TMD) and headache are complex. This study aims to assess the association between TMD, headache, and psychological dimensions such as psychological inflexibility and pain acceptance. The sample consisted of 120 participants following a non-probabilistic convenience sampling strategy through a direct invitation to the patients attending our facilities and their relatives ( = 61 diagnosed with headache, = 34 diagnosed with TMD-headache, = 25 control group).

Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques.

Rhesus macaques () are the most widely distributed species of Old World monkey and are frequently used as animal models to study human health and disease. Their gastrointestinal microbial community likely plays a major role in their physiology, ecology and evolution. Herein, we compared the fecal microbiome and antibiotic resistance genes in 15 free-ranging and 81 zoo-captive rhesus macaques sampled from two zoos in China, using both 16S amplicon sequencing and whole genome shotgun DNA sequencing approaches.

Key Technologies for Progressing Discovery of Microbiome-Based Medicines.

A growing number of experimental and computational approaches are illuminating the "microbial dark matter" and uncovering the integral role of commensal microbes in human health. Through this work, it is now clear that the human microbiome presents great potential as a therapeutic target for a plethora of diseases, including inflammatory bowel disease, diabetes and obesity. The development of more efficacious and targeted treatments relies on identification of causal links between the microbiome and disease; with future progress dependent on effective links between state-of-the-art sequencing approaches, computational analyses and experimental assays.

Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium.

The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member.

The microbiome and host mucosal interactions in urinary tract diseases.

The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system.

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.

There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. The pipeline substantially outperforms other commonly used software in identifying bacteria and fungi and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms.

Corrigendum: Whole Genome Sequencing of Australian Isolates Reveals Genetic Diversity and Novel Sequence Types.

[This corrects the article DOI: 10.3389/fmicb.2018.

Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes.

Background: Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria.

Whole Genome Sequencing of Australian Isolates Reveals Genetic Diversity and Novel Sequence Types.

is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of in Australia.

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta).

Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order.

Highly structured prokaryote communities exist within the skeleton of coral colonies.

Physiological performance, disease and bleaching prevalence are often patchy within individual coral colonies. These responses are largely influenced by coral-associated microbes, but how the coral microbiome changes over small spatial scales has never been quantified before. We performed a high-resolution quantification of the spatial scale of microbial species turnover (β-diversity) within skeletons of boulder-forming Porites corals.

Diversity and stability of coral endolithic microbial communities at a naturally high pCO reef.

The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp.

Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data.

The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon sampling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here, we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp.

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae.

Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers (tufA, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples.

Ecological niche models of invasive seaweeds.

Ecological niche models (ENMs) are commonly used to calculate habitat suitability from species' occurrence and macroecological data. In invasive species biology, ENMs can be applied to anticipate whether invasive species are likely to establish in an area, to identify critical routes and arrival points, to build risk maps and to predict the extent of potential spread following an introduction. Most studies using ENMs focus on terrestrial organisms and applications in the marine realm are still relatively rare.

Infrared assisted production of 3,4-dihydro-2(1H)-pyridones in solvent-free conditions.

A green approach for the synthesis of a set of ten 4-aryl substituted-5-alcoxy carbonyl-6-methyl-3,4-dihydro-2(1H)-pyridones using Meldrum's acid has been devised, the absence of solvent and the activation with infrared irradiation in addition to a multicomponent protocol are the main reaction conditions. The transformations proceeded with moderated yields (50-75%) with a reasonable reaction rate (3 h). It is worth noting that two novel molecules of the new class of the bis-3,4-dihydropyridones were also obtained.