4.8 Article

Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

clinker & clustermap.js: automatic generation of gene cluster comparison figures

Cameron L. M. Gilchrist et al.

Summary: Genes involved in biological pathways are often found in gene clusters, and comparing these clusters can provide valuable insights into their function and evolutionary history. To simplify the tedious process of comparing and visualizing gene cluster similarity, a Python tool called clinker and a companion JavaScript library called clustermap.js have been developed to automatically generate accurate, interactive, publication-quality gene cluster comparison figures from sequence files.

BIOINFORMATICS (2021)

Article Microbiology

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Christine He et al.

Summary: The study reveals the influence of groundwater geochemistry on the distribution and abundance of CPR bacteria and DPANN archaea; significant species-level differences exist among CPR and DPANN communities across different groundwater sites; cryogenic transmission electron microscopy imaging and genomic analyses are useful in studying the species and growth patterns of these microbes.

NATURE MICROBIOLOGY (2021)

Article Cell Biology

Streptococcus pyogenes upregulates arginine catabolism to exert its pathogenesis on the skin surface

Yujiro Hirose et al.

Summary: The ADI pathway in Streptococcus pyogenes enhances bacterial survival and pathogenicity under low-glucose conditions by altering gene expression, particularly by upregulating virulence genes. By increasing the expression of virulence genes, including those encoding exotoxins, S. pyogenes augments its pathogenicity through the ADI pathway. Furthermore, arginine from filaggrin in the stratum corneum serves as a key substrate for the ADI pathway, promoting the pathogenicity of S. pyogenes on the skin.

CELL REPORTS (2021)

Article Microbiology

Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria

Alexander L. Jaffe et al.

Summary: The study found that the transitions of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.
Article Dentistry, Oral Surgery & Medicine

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts

B. Bor et al.

JOURNAL OF DENTAL RESEARCH (2020)

Article Biotechnology & Applied Microbiology

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Alon Shaiber et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees

Balakrishnan Subramanian et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Genetics & Heredity

Genomic features of bacterial adaptation to plants

Asaf Levy et al.

NATURE GENETICS (2018)

Review Biochemistry & Molecular Biology

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

Cindy J. Castelle et al.

Review Genetics & Heredity

Population genomics of bacterial host adaptation

Samuel K. Sheppard et al.

NATURE REVIEWS GENETICS (2018)

Article Biotechnology & Applied Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host

Batbileg Bor et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Dentistry, Oral Surgery & Medicine

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation

M. Agnello et al.

JOURNAL OF DENTAL RESEARCH (2017)

Article Multidisciplinary Sciences

The evolution of host-symbiont dependence

Roberta M. Fisher et al.

NATURE COMMUNICATIONS (2017)

Article Microbiology

A new view of the tree of life

Laura A. Hug et al.

NATURE MICROBIOLOGY (2016)

Review Dentistry, Oral Surgery & Medicine

Oral Microbiome Metabolism: From Who Are They? to What Are They Doing?

N. Takahashi

JOURNAL OF DENTAL RESEARCH (2015)

Article Ecology

Parasite host range and the evolution of host resistance

F. A. Gorter et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2015)

Article Multidisciplinary Sciences

Unusual biology across a group comprising more than 15% of domain Bacteria

Christopher T. Brown et al.

NATURE (2015)

Review Genetics & Heredity

Horizontal gene transfer: building the web of life

Shannon M. Soucy et al.

NATURE REVIEWS GENETICS (2015)

Article Multidisciplinary Sciences

Migration and horizontal gene transfer divide microbial genomes into multiple niches

Rene Niehus et al.

NATURE COMMUNICATIONS (2015)

Article Multidisciplinary Sciences

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

Xuesong He et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Dentistry, Oral Surgery & Medicine

Oral Arginine Metabolism May Decrease the Risk for Dental Caries in Children

M. M. Nascimento et al.

JOURNAL OF DENTAL RESEARCH (2013)

Article Multidisciplinary Sciences

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

Gerald Schoenknecht et al.

SCIENCE (2013)

Review Endocrinology & Metabolism

Arginine de novo and nitric oxide production in disease states

Yvette C. Luiking et al.

AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM (2012)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Multidisciplinary Sciences

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

Jan-Hendrik Hehemann et al.

NATURE (2010)

Article Dentistry, Oral Surgery & Medicine

Correlations of oral bacterial arginine and urea catabolism with caries experience

M. M. Nascimento et al.

ORAL MICROBIOLOGY AND IMMUNOLOGY (2009)

Article Dentistry, Oral Surgery & Medicine

Caries Ecology Revisited: Microbial Dynamics and the Caries Process

N. Takahashi et al.

CARIES RESEARCH (2008)

Article Chemistry, Multidisciplinary

Inactivation of microbial arginine deiminases by L-canavanine

Ling Li et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Review Microbiology

From soil to gut:: Bacillus cereus and its food poisoning toxins

Lotte P. Stenfors Arnesen et al.

FEMS MICROBIOLOGY REVIEWS (2008)

Review Microbiology

Horizontal gene transfer, genome innovation and evolution

JP Gogarten et al.

NATURE REVIEWS MICROBIOLOGY (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Multidisciplinary Sciences

Transfer of photosynthesis genes to and from Prochlorococcus viruses

D Lindell et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Microbiology

Surviving the acid test: Responses of gram-positive bacteria to low pH

PD Cotter et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2003)