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Journal of Bacteriology Oct 2010The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are...
The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.
Topics: Actinobacteria; Bacteria; Bacteroidetes; Chlamydia; Chloroflexi; Fusobacteria; Humans; Metagenome; Molecular Sequence Data; Mouth; Phylogeny; Proteobacteria; RNA, Ribosomal, 16S; Spirochaetales
PubMed: 20656903
DOI: 10.1128/JB.00542-10 -
PLoS Neglected Tropical Diseases May 2019The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the...
The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected worldwide and we have redefined the classification of species in the genus. The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined but our data also provide new insights into the emergence of virulence in the pathogenic species.
Topics: Animals; Asia; Evolution, Molecular; Genome, Bacterial; Genomics; Humans; Leptospira; Leptospirosis; Phylogeny; Virulence; Zoonoses
PubMed: 31120895
DOI: 10.1371/journal.pntd.0007270 -
Biomolecules Apr 2020Spirochetes can be distinguished from other flagellated bacteria by their long, thin, spiral (or wavy) cell bodies and endoflagella that reside within the periplasmic... (Review)
Review
Spirochetes can be distinguished from other flagellated bacteria by their long, thin, spiral (or wavy) cell bodies and endoflagella that reside within the periplasmic space, designated as periplasmic flagella (PFs). Some members of the spirochetes are pathogenic, including the causative agents of syphilis, Lyme disease, swine dysentery, and leptospirosis. Furthermore, their unique morphologies have attracted attention of structural biologists; however, the underlying physics of viscoelasticity-dependent spirochetal motility is a longstanding mystery. Elucidating the molecular basis of spirochetal invasion and interaction with hosts, resulting in the appearance of symptoms or the generation of asymptomatic reservoirs, will lead to a deeper understanding of host-pathogen relationships and the development of antimicrobials. Moreover, the mechanism of propulsion in fluids or on surfaces by the rotation of PFs within the narrow periplasmic space could be a designing base for an autonomously driving micro-robot with high efficiency. This review describes diverse morphology and motility observed among the spirochetes and further summarizes the current knowledge on their mechanisms and relations to pathogenicity, mainly from the standpoint of experimental biophysics.
Topics: Flagella; Movement; Periplasm; Spirochaetales
PubMed: 32260454
DOI: 10.3390/biom10040550 -
Microbes and Infection Dec 2019
Topics: Adaptation, Physiological; Artifacts; Cell Culture Techniques; Host-Pathogen Interactions; Leptospira; Leptospirosis; Models, Biological
PubMed: 31226394
DOI: 10.1016/j.micinf.2019.06.001 -
Trends in Microbiology Mar 2023Spirochaetes, a phylum that includes medically important pathogens such as the causative agents of Lyme disease, syphilis, and leptospirosis, are in many ways highly... (Review)
Review
Spirochaetes, a phylum that includes medically important pathogens such as the causative agents of Lyme disease, syphilis, and leptospirosis, are in many ways highly unique bacteria. Their cell morphology, subcellular organization, and metabolism reveal atypical features. Spirochetal motility is also singular, dependent on the presence of periplasmic flagella or endoflagella, inserted subterminally at cell poles and not penetrating the outer membrane and elongating outside the cell as in enterobacteria. In this review we present a comprehensive comparative genomics analysis of endoflagellar systems in spirochetes, highlighting recent findings on the flagellar basal body and filament. Continued progress in understanding the function and architecture of spirochetal flagella is uncovering paradigm-shifting mechanisms of bacterial motility.
Topics: Humans; Spirochaetales; Lyme Disease; Flagella; Bacterial Proteins
PubMed: 36244923
DOI: 10.1016/j.tim.2022.09.010 -
Journal of Clinical Laboratory Analysis May 2022Spirochetes are a large group of prokaryotes that originated from Gram-negative bacteria and are capable of causing a variety of human and animal infections. However,... (Review)
Review
Spirochetes are a large group of prokaryotes that originated from Gram-negative bacteria and are capable of causing a variety of human and animal infections. However, the pathogenesis of spirochetes remains unclear, as different types of spirochetes play pathogenic roles through different pathogenic substances and mechanisms. To survive and spread in the host, spirochetes have evolved complicated strategies to evade host immune responses. In this review, we aimed to provide a comprehensive overview of immune evasion strategies in spirochetes infection. These strategies can be explained from the following points: (i) Antigenic variation: random, unidirectional, and segmental conversion of the gene to evade immune surveillance; (ii) Overcoming the attack of the complement system: recruitment of host complement regulators, cleavage of complement components and inhibition of complement activation to evade immune defenses; (iii) Interfering with immune cells to regulating the immune system; (iv) Persistent infection: invading and colonizing the host cell to escape immune damage.
Topics: Animals; Complement System Proteins; Humans; Immune Evasion; Immunity; Spirochaetales
PubMed: 35403248
DOI: 10.1002/jcla.24414 -
Microbiology Spectrum May 2019Spirochetes form a separate phylum of bacteria with two membranes but otherwise unusual morphologies and envelope structures. Distinctive common features of , , and...
Spirochetes form a separate phylum of bacteria with two membranes but otherwise unusual morphologies and envelope structures. Distinctive common features of , , and include the sequestration of flagella to the periplasm and thin peptidoglycan cell walls that are more closely associated with the inner membrane. Outer membrane compositions differ significantly between the genera. most closely track Gram-negative bacteria due to the incorporation of lipopolysaccharides. and outer membranes lack lipopolysaccharide, with treponemes expressing only a few outer membrane proteins and displaying a dizzying diversity of abundant surface lipoproteins instead. Phylogenetic and experimental evidence indicates that spirochetes have adapted various modules of bacterial export and secretion pathways to build and maintain their envelopes. Export and insertion pathways in the inner membrane appear conserved, while spirochetal experimentation with various envelope architectures over time has led to variations in secretion pathways in the periplasm and outer membrane. Classical type I to III secretion systems have been identified, with demonstrated roles in drug efflux and export of flagellar proteins only. Unique activities of periplasmic proteases, including a C-terminal protease, are involved in maturation of some periplasmic proteins. Proper lipoprotein sorting within the periplasm appears to be dependent on functional Lol pathways that lack the outer membrane lipoprotein insertase LolB. The abundance of surface lipoproteins in and detailed protein sorting studies suggest a lipoprotein secretion pathway that either extends Lol through the outer membrane or bypasses it altogether. Proteins can be released from cells in outer membrane vesicles or, rarely, as soluble proteins.
Topics: Bacteria; Bacterial Outer Membrane; Bacterial Outer Membrane Proteins; Biological Transport; Cell Membrane; Lipopolysaccharides; Lipoproteins; Periplasm; Phylogeny; Protein Sorting Signals; Protein Transport; Spirochaetales
PubMed: 31198130
DOI: 10.1128/microbiolspec.PSIB-0026-2019 -
Seminars in Cell & Developmental Biology Oct 2015Bacterial pathogens are often classified by their toxicity and invasiveness. The invasiveness of a given bacterium is determined by how capable the bacterium is at... (Review)
Review
Bacterial pathogens are often classified by their toxicity and invasiveness. The invasiveness of a given bacterium is determined by how capable the bacterium is at invading a broad range of tissues in its host. Of mammalian pathogens, some of the most invasive come from a group of bacteria known as the spirochetes, which cause diseases, such as syphilis, Lyme disease, relapsing fever and leptospirosis. Most of the spirochetes are characterized by their distinct shapes and unique motility. They are long, thin bacteria that can be shaped like flat-waves, helices, or have more irregular morphologies. Like many other bacteria, the spirochetes use long, helical appendages known as flagella to move; however, the spirochetes enclose their flagella in the periplasm, the narrow space between the inner and outer membranes. Rotation of the flagella in the periplasm causes the entire cell body to rotate and/or undulate. These deformations of the bacterium produce the force that drives the motility of these organisms, and it is this unique motility that likely allows these bacteria to be highly invasive in mammals. This review will describe the current state of knowledge on the motility and biophysics of these organisms and provide evidence on how this knowledge can inform our understanding of spirochetal diseases.
Topics: Animals; Biophysical Phenomena; Flagella; Host-Pathogen Interactions; Humans; Models, Biological; Movement; Periplasm; Spirochaetales; Spirochaetales Infections
PubMed: 26481969
DOI: 10.1016/j.semcdb.2015.10.015 -
Nihon Saikingaku Zasshi. Japanese... 2014Spirochetes have flagella within the cell body and swim by wriggling the spiral cell body. Besides they have been known to be critical agents causing various infectious... (Review)
Review
Spirochetes have flagella within the cell body and swim by wriggling the spiral cell body. Besides they have been known to be critical agents causing various infectious diseases, their eccentric appearances and motilities have been attracting many scientists in a wide variety of fields other than bacteriologists. Unlike externally flagellated bacteria that swim by using flagella as a screw propeller, spirochetes progress in a liquid by changing their cell shapes. To understand the unique motion mechanism of spirochetes, many experiments and theoretical studies are being carried out. In this review, I will summarize morphological and motile properties of various species of spirochete, such as Borrelia, Treponema and Brachyspira. I will also expound on the motion mechanism of Leptospira with our latest results obtained by high-resolution optical photometry.
Topics: Borrelia; Brachyspira; Flagella; Leptospira; Microscopy; Movement; Spirochaetales; Treponema
PubMed: 25186643
DOI: 10.3412/jsb.69.527 -
Cell Host & Microbe Nov 2021Lyme disease, which is caused by the spirochete Borrelia burgdorferi, is on the rise. Current treatment relies on broad-spectrum antibiotics that perturb the gut...
Lyme disease, which is caused by the spirochete Borrelia burgdorferi, is on the rise. Current treatment relies on broad-spectrum antibiotics that perturb the gut microbiome. In a recent paper in Cell, Leimer et al. demonstrate the utility of a long-forgotten antibiotic, Hygromycin A, as a spirochete-specific antibacterial that is conducive to gut health.
Topics: Borrelia burgdorferi; Borrelia burgdorferi Group; Cinnamates; Humans; Hygromycin B; Lyme Disease
PubMed: 34762823
DOI: 10.1016/j.chom.2021.10.007