Elevated rates of horizontal gene transfer in the industrialized human microbiome

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Shedding light onto the genera (Mollusca : Nudibranchia) Kaloplocamus and Plocamopherus with description of new species belonging to these unique bioluminescent dorids

Volume: 48Start Page: 178End Page: 20

Lophotrochozoan mitochondrial genomes

Progress in both molecular techniques and phylogenetic methods has challenged many of the interpretations of traditional taxonomy. One example is in the recognition of the animal superphylum Lophotrochozoa (annelids, mollusks, echiurans, platyhelminthes, brachiopods, and other phyla), although the relationships within this group and the inclusion of some phyla remain uncertain. While much of this progress in phylogenetic reconstruction has been based on comparing single gene sequences, we are beginning to see the potential of comparing large-scale features of genomes, such as the relative order of genes. Even though tremendous progress is being made on the sequence determination of whole nuclear genomes, the dataset of choice for genome-level characters for many animals across a broad taxonomic range remains mitochondrial genomes. We review here what is known about mitochondrial genomes of the lophotrochozoans and discuss the promise that this dataset will enable insight into their relationships

Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species

The large degree of morphological variations, particularly amongst juveniles, has led to inconsistencies in the literature regarding the taxonomic status of Amphithrax aculeatus (Herbst, 1790) and Amphithrax verrucosus (H. Milne Edwards, 1832). As a result of recent biodiversity sampling initiatives in Barbados, West Indies, multiple specimens of Amphithrax aculeatus and A. verrucosus have been collected. This has prompted us to undertake a thorough reassessment of their morphological and molecular characteristics. Moreover, morphological differences in the carapace, antennae, chelipeds, pereopods and the male first gonopod (G1) supports A. aculeatus and A. verrucosus as separate species. Molecular phylogenetic analysis, based on newly-generated sequences of the 12S rRNA, 16S rRNA and ITS-1 genes also shows that A. verrucosus is a separate species and sister taxa to A. aculeatus. The total number of species within the genus Amphithrax is now brought to eleven. However, our molecular analysis also shows that the taxonomic placement of Amphithrax armatus (Saussure, 1853) within Amphithrax is questionable

Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species

The large degree of morphological variations, particularly amongst juveniles, has led to inconsistencies in the literature regarding the taxonomic status of Amphithrax aculeatus (Herbst, 1790) and Amphithrax verrucosus (H. Milne Edwards, 1832). As a result of recent biodiversity sampling initiatives in Barbados, West Indies, multiple specimens of Amphithrax aculeatus and A. verrucosus have been collected. This has prompted us to undertake a thorough reassessment of their morphological and molecular characteristics. Moreover, morphological differences in the carapace, antennae, chelipeds, pereopods and the male first gonopod (G1) supports A. aculeatus and A. verrucosus as separate species. Molecular phylogenetic analysis, based on newly-generated sequences of the 12S rRNA, 16S rRNA and ITS-1 genes also shows that A. verrucosus is a separate species and sister taxa to A. aculeatus. The total number of species within the genus Amphithrax is now brought to eleven. However, our molecular analysis also shows that the taxonomic placement of Amphithrax armatus (Saussure, 1853) within Amphithrax is questionable

Associations between Polycystic Ovary Syndrome (PCOS) and Antibiotic Use: Results from the UAEHFS

Peer reviewed: TrueAcknowledgements: The authors would like to thank all members of the Public Health Research Center at New York University Abu Dhabi and those who are actively involved in the UAE Healthy Future Study (UAEHFS). This study would not have been possible without their collective effort.Publication status: PublishedWomen with polycystic ovary syndrome (PCOS) have a higher susceptibility to infections compared to those without PCOS. Studies evaluating antibiotic use based on PCOS status are scarce. Therefore, we aimed to (i) assess the associations between self-reported PCOS and antibiotic use, and (ii) whether PCOS treatment and the age at PCOS diagnosis modified the associations above. This cross-sectional analysis used the United Arab Emirates Healthy Future Study (UAEHFS) conducted from February 2016 to March 2023 involving 2063 Emirati women aged 18–62 years. We performed ordinal logistic regressions under unadjusted and demographic-health-characteristic-adjusted models to obtain the odds ratios (ORs) and 95% confidence intervals (CIs) to analyze PCOS and antibiotic use. Subgroup analyses were performed by treatment status and age at diagnosis. We found that women with PCOS were 55% more likely to frequently take a course of antibiotics in the past year (aOR 1.55; 95% CI 1.26–1.90). Similar likelihoods were also found among those being treated for PCOS and those without treatment but with a PCOS diagnosis at ≤25 years. Our study suggests that PCOS was associated with an increased use of antibiotics among Emirati women. Understanding the frequent antibiotic use susceptibility among those with PCOS may improve antibiotic use surveillance and promote antibiotic stewardship in these at-risk individuals.</jats:p