Microbial Genomics - Science topic

Keywords Microbial genomics CAZYmes Vitamins Resistome Copyright This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY). Abstract Lactiplantibacillus plantarum is a highly adaptable and versatile species that can be found in a diverse range of niches. It can generate bioactiv...

Helicobacter pylori is a significant human pathogen associated with gastric diseases, yet the role of plasmids in its pathogenicity remains underexplored. This study provides a comprehensive genomic and functional characterization of the H. pylori plasmidome using publicly available plasmid sequences. Of 335 plasmids analyzed, 127 non-redundant rep...

Periodic table of chemical elements serves as the foundation of material chemistry, impacting human health in many different ways. It contributes to the creation, growth, and manipulation of functional metallic, ceramic, metalloid, polymeric, and carbon‐based materials on and near an atomic scale. Recent nanotechnology advancements have revolutioni...

Insects, with over a million species, exhibit intricate associations with microorganisms, particularly in their gut microbiota. The insect gut microbiota, comprising bacteria, fungi, viruses, and protozoa, significantly influences nutrient digestion, metabolism and immune system modulation. From harmful parasites to beneficial mutualists, symbiotic...

Genomes encode elaborate networks of genes whose products must seamlessly interact to support living organisms. Humans’ capacity to understand these biological systems is limited by their sheer size and complexity. In this article, we develop a proof of concept framework for training a machine learning (ML) algorithm to model bacterial genome compo...

Here, we report the draft genome sequences of Flagellimonas sp. MMG031 and Marinobacter sp. MMG032, isolated from coral-associated dinoflagellate Symbiodinium pilosum, assembled and analyzed by undergraduate students participating in a Marine Microbial Genomics (MMG) course. A genomic comparison suggests MMG031 and MMG032 are novel species and a re...

Microorganisms play a pivotal role in agricultural ecosystems, contributing significantly to soil health, crop productivity, and sustainable farming practices. This review explores the multifaceted functions of soil microorganisms, including bacteria, fungi, and archaea, in enhancing nutrient cycling, improving soil structure, and promoting plant g...

Background Cyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis , has been studied for biomass pyrolysis, estrogen degradation, and the production of bioethanol, monosaccharide, and phycocyanin. To better un...

Large double-stranded DNA viruses of the phylum Nucleocytoviricota (Giant Viruses; GVs) are the largest known viruses, infecting various eukaryotic hosts, particularly protists and algae. These viruses impact biogeochemical cycles and host genome evolution but are challenging to identify and classify due to their complex genomes. We present GVClass...

Vaginal odor is a natural and dynamic phenomenon influenced by a complex interplay of genetic, microbial, and cultural factors. While often misunderstood or stigmatized, vaginal odor is primarily shaped by the composition of the vaginal microbiota, with beneficial Lactobacillus species playing a crucial role in maintaining a healthy, low-pH environ...

Christensenella minuta is one of the representative bacterial species of the human gut microbiome. We report the complete genome sequence of two strains, Christensenella minuta CIP 112228 and CIP 112229, isolated from two healthy volunteers.

Background: A non-endoscopic capsule-sponge device allows sampling the entire length of the esophagus. Here, we compared microbiomes of the oral cavity, esophagus, and gastric corpus collected by oral swab, capsule-sponge device, and endoscopic biopsy, respectively, in patients representing three distinct risk profiles for esophageal squamous cell...

Background To what degree a string of symbols can be compressed reveals important details about its complexity. For instance, strings that are not compressible are random and carry a low information potential while the opposite is true for highly compressible strings. We explore to what extent microbial genomes are amenable to compression as they v...

Genomic surveillance enables the early detection of pathogen transmission in healthcare facilities and contributes to the reduction of substantial patient harm. Fast turnaround times, flexible multiplexing, and low capital requirements make Nanopore sequencing well suited for genomic surveillance purposes; the analysis of Nanopore data, however, ca...

We reviewed all diagnoses of Shigella species notified to the UK Health Security Agency from January 2016 to March 2023. An overall increase in notifications of shigellosis was seen between 2016 (n = 415/quarter) and 2023 (n = 1 029/quarter). However, notifications dramatically declined between March 2020 and September 2021 during the COVID-19 pand...

Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing te...

In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new ‘phylepic’ visualization that combines a phylo...

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and techn...

Background The number of cholera cases reported to the World Health Organization (WHO) in 2022 was more than double that of 2021. Nine countries of the WHO European Region reported 51 cases of cholera in 2022 vs five reported cases in 2021. Aim We aimed to confirm that the Vibrio cholerae O1 isolates reported by WHO European Region countries in 20...

Background Cyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis , has been studied for biomass pyrolysis, estrogen degradation, and the production of bioethanol, monosaccharide, and phycocyanin. To better un...

The lungs, as vital organs in the human body, continuously engage in gas exchange with the external environment. The lung microbiota, a critical component in maintaining internal homeostasis, significantly influences the onset and progression of diseases. Beneficial interactions between the host and its microbial community are essential for preserv...

Background Large double-stranded DNA viruses of the phylum Nucleocytoviricota (Giant viruses; GVs) include the largest known viruses, both in terms of capsid and genome size and are associated with a wide range of eukaryotic hosts. The ones able to infect protists and algae have been shown to be the dominant orders of GVs in the environmental sampl...

The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a...

Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods an...

Abstract: This chapter explores the transformative potential of microbial biotechnology in addressing some of the most pressing ecological challenges of our time. It delves into the diverse applications of microbes in environmental sustainability, agriculture, and industry, highlighting their role in processes such as bioremediation, biofuel produ...

Genomic epidemiology is a transformative field that integrates microbial genomics with epidemiological data to enhance the understanding, prevention, and control of infectious diseases. The advent of next-generation sequencing (NGS) technologies has made it possible to rapidly sequence microbial genomes, providing detailed insights into the transmi...

Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Her...

Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Her...

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate ind...

Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic trai...

The analysis and comparison of genomes rely on different tools for tasks such as annotation, orthology prediction, and phylogenetic inference. Most tools are specialized for a single task, and additional efforts are necessary to integrate and visualize the results. To fill this gap, we developed zDB, an application integrating a Nextflow analysis pipel...

Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site...

Microbial forensics is a new discipline of science that analyzes evidence related to biological crime through the uniqueness and abundance of microorganisms and their toxins. Microorganisms remain alive longer than any other trace of biological evidence, such as DNA, fingerprints, and fibers, because of the protective cell membrane or capsules. Mic...

In recent years, the analysis of metagenomic data to recover unculturable microbes has revolutionized microbial genomics by rapidly expanding the reference genome catalog. Central to this, are the computational approaches of de novo assembly and genome binning that enable large-scale reference-independent recovery of microbial genomes from the meta...

Genomic analyses of bacterial isolates are effective to compare the prevalence of antibiotic resistance genes and virulence determinants in different contexts. This study provides a comprehensive genomic description of 339 Staphylococcus aureus strains isolated from patients with bacteremia (2014–2022). Nosocomial acquisition accounted for 56.6% of...

Time-restricted eating (TRE) is a promising obesity management strategy, but weight-loss efficacy varies among participants, and the underlying mechanism is unclear. The study aimed to investigate the role of gut microbiota in weight-loss response during long-term TRE intervention. We analyzed data from 51 obese adults in a 12-month TRE program, ca...

In 2003−2023, amid 5,436 Acinetobacter baumannii isolates collected globally through the Multidrug-Resistant Organism Repository and Surveillance Network, 97 were ST19 PAS , 34 of which carbapenem-resistant. Strains (n = 32) sampled after 2019 harboured either bla OXA-23 , bla OXA-72 , and/or bla NDM-5 . Phylogenetic analysis of the 97 isolates and...

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a rep...

The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across large genomic databases or user-generated datasets remains a challenge. Here, we introduce AnnoView, a web server...

Staphylococcus aureus asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 S . aureus was associated with 20 000 deaths in the USA alone. Dividing S. aureus isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despit...

Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile riboty...

In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic...

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical...

The present study was undertaken to profile and compare the cecal microbial communities in conventionally (CONV) grown and raised without antibiotics (RWA) broiler chickens. Three hundred chickens were collected from five CONV and five RWA chicken farms on days 10, 24, and 35 of age. Microbial genomic DNA was extracted from cecal contents, and the...

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate ind...

Accurate annotation to single-nucleotide resolution of the transcribed regions in genomes is key to optimally analyse RNA-seq data, understand regulatory events and for the design of experiments. However, currently most genome annotations provided by GenBank generally lack information about untranslated regions. Additionally, information regarding...

This prospective study aimed to determine the prevalence of long COVID in patients hospitalized for SARS-CoV-2 infection from March 2020 to July 2022 and assess the impact of different viral lineages. A total of 2,524 patients were followed up for 12 months, with persistent symptoms reported in 35.2% at one month, decreasing thereafter. Omicron var...

As the issue of traditional antibiotic resistance continues to worsen, exploring new antimicrobial substances has become crucial to addressing this challenge. Antimicrobial peptides (AMPs), recognized for their low resistance levels and minimal bacterial mutation frequencies, have garnered significant attention from researchers. However, traditiona...

Here, we report the draft genome sequence of Exiguobacterium sp. strain MMG028, isolated from Rose Creek, San Diego, CA, USA, assembled and analyzed by undergraduate students participating in a marine microbial genomics course. A genomic comparison suggests that MMG028 is a novel species, providing a resource for future microbiology and biotechnolo...

N,N-Diethyl-3-toluamide (DEET) is a commonly used insect repellent, which acts as an organic chemical contaminant in water and considered as an emerging contaminant which has been observed worldwide. It gets discharged into the environment through sewage waste. The various methods have been used to degrade DEET, such as UV based, ozonation, photoca...

The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC’s biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.

Growing evidence has demonstrated that cold and humid environmental stress triggers gastrointestinal (GI) disorders. In this study, we explored the effects of intestinal microbiota homeostasis on the intestinal mucus barrier and GI disorders by cold and humid environmental stress. Moreover, the inner link between the intestinal mucosal microbiota a...

Fermented foods such as table olives are produced through a spontaneous process that has been improved over the years, ensuring the safety and quality of the final product. The aim of the present work was to study the action of starter cultures of lactic acid bacteria (Lacticaseibacillus rhamnosus GG ATCC53103, Levilactobacillus brevis ATCC8287, an...

Sulfitobacter is a bacterium recognized for its production of AMP-independent sulfite oxidase, which is instrumental in the creation of sulfite biosensors. This capability underscores its ecological and economic relevance. In this study, we present a newly discovered phage, Sulfitobacter phage vB_SupP_AX, which was isolated from Maidao of Qingdao,...

Combat extremity wounds are highly susceptible to contamination from surrounding environmental material. This bioburden could be partially transferred from materials in immediate proximity to the wound, including fragments of the uniform and gear. However, the assessment of the microbial bioburden present on military gear during operational conditi...

Microbial secondary metabolites are usually synthesized by colocalized genes termed biosynthetic gene clusters (BGCs). A large portion of BGCs remain undiscovered in microbial genomes and metagenomes, representing a pressing challenge in unlocking the full potential of natural product diversity. In this work, we propose BGC-Prophet, a language mode...

Background Cholera is a bacterial infection caused by the ingestion of contaminated water or food. It principally affects the gastrointestinal system and spreads easily, causing outbreaks. The first case of cholera in this outbreak was detected in Lebanon in October 2022. The outbreak lasted three months, with 8,007 suspected cases (671 laboratory-...

In recent years, interdisciplinary research has gained great importance because it has much in common with new advances in science. Technologies that allow for technological breakthroughs and advanced development of scientific and technical groundwork for the development of fundamentally new materials (products), technologies at the junction of var...

Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, nation...

Current diagnostics and clinical management strategies for combat wounds are based on decisions made by expert clinicians. However, even in the hands of experienced surgeons, wounds from combat injuries can exhibit failed healing and complications related to limitations in the rapid and comprehensive generation of diagnostic information. Previous s...

Growing evidence has demonstrated that cold and humid environmental stress triggers gastrointestinal (GI) disorders. In this study, we explored the effects of intestinal microbiota homeostasis on the intestinal mucus barrier and GI disorders by cold and humid environmental stress. Moreover, the inner link between the intestinal mucosal microbiota a...

Enterococcus faecalis is a commensal bacterium of the human gastrointestinal tract that causes opportunistic infections. The E. faecalis genetic changes associated with pathogenicity, particularly gut-to-bloodstream translocation, remain poorly understood. Here, we performed a genome-wide association study (GWAS) of 736 whole-genome sequences of fe...

Leptospirosis is a worldwide zoonotic disease. The annual incidence of the disease varies across the globe and it is more common in tropical region. PALAPES are chosen for this study since their activities involved rigorous military exercise which can expose them to leptospiral infection from the environment. Objective: The objective of this s...

The climate crisis and years of unsustainable agricultural practices have reduced soil fertility and crop yield. In addition, agricultural lands contribute more than 10% of greenhouse gases (GHGs). These concerns can be addressed by using biochar for carbon neutralization, environmental restoration, and agricultural management. Biochar has a role i...

Background Soil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metage...

Analyzing the data deluge generated by next generation sequencing technologies is a challenging task. Variant calling aids in characterizing phenotype of an organism. The objective of this work is to compare popular variant calling protocols available in terms of their accuracy for human and microbial genomes. Three popular read aligners viz. BWA-M...