Publications

treponema succinifaciens sp. nov., an anaerobic spirochete from the swine intestine.	the morphology, the general physiological characteristics, and the energy-yielding metabolism of an obligately anaerobic spirochete isolated from the colon of a swine were studied. electron microscopy showed that the helical spirochetal cells possessed an outer sheath, a protoplasmic cylinder, and 4 periplasmic fibrils in a 2-4-2 arrangement. the spirochete grew in an atmosphere of n2 in prereduced media containing a carbohydrate, nahco3, rumen fluid, yeast extract, peptone, l-cysteine, and inor ...	1979	120726
enzymatic activities for interconversion of purines in spirochetes.	enzymatic activities that catalyze the interconversion of purines and purine derivatives were detected in cell extracts of spirochaeta aurantia, spirochaeta stenostrepta, treponema succinifaciens, and treponema denticola. phosphoribosyltransferase activities present in cell extracts of each of the four spirochete species functioned in the conversion of adenine, hypoxanthine, and guanine to amp, imp, and gmp, respectively. nucleotidase activities in the extracts mediated the formation of nucleosi ...	1982	6292162
detection and identification of treponema hyodysenteriae by using oligodeoxynucleotide probes complementary to 16s rrna.	oligodeoxynucleotide probes (17 and 28 bases long) complementary to a unique region of treponema hyodysenteriae 16s rrna were developed. these probes bound specifically to partially purified rrna and whole-cell rrna of t. hyodysenteriae. no binding to partially purified rrna or whole-cell rrna of treponema innocens, treponema succinifaciens, treponema bryantii, or escherichia coli occurred under stringent conditions. the 28-base probe was 5 to 10 times more sensitive than the 17-base probe when ...	1990	1704013
reclassification of treponema hyodysenteriae and treponema innocens in a new genus, serpula gen. nov., as serpula hyodysenteriae comb. nov. and serpula innocens comb. nov.	the intestinal anaerobic spirochetes treponema hyodysenteriae b78t (t = type strain), b204, b169, and a-1, treponema innocens b256t and 4/71, treponema succinifaciens 6091t, and treponema bryantii rus-1t were compared by performing dna-dna reassociation experiments, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of cell proteins, restriction endonuclease analysis of dna, and 16s rrna sequence analysis. dna-dna relative reassociation experiments in which the s1 nuclease method was used ...	1991	1704792
phylogenetic analysis of the spirochetes.	the 16s rrna sequences were determined for species of spirochaeta, treponema, borrelia, leptospira, leptonema, and serpula, using a modified sanger method of direct rna sequencing. analysis of aligned 16s rrna sequences indicated that the spirochetes form a coherent taxon composed of six major clusters or groups. the first group, termed the treponemes, was divided into two subgroups. the first treponeme subgroup consisted of treponema pallidum, treponema phagedenis, treponema denticola, a thermo ...	1991	1917844
characterization of serpulina (treponema) hyodysenteriae and related intestinal spirochetes by ribosomal rna gene restriction patterns.	serpulina (treponema) hyodysenteriae strain a-1 partially purified rrna, labelled with photobiotin, was used as a non-radioactive probe to identify the rrna gene restriction patterns of s. hyodysenteriae strains and other spirochetes. sau3a restriction enzyme digests resulted in similar rrna gene restriction patterns in s. hyodysenteriae strains from five different countries. some s. hyodysenteriae strains could be differentiated by variations in their rrna gene restriction patterns after cleava ...	1992	1354196
identification and partial characterization of a group of weakly beta-hemolytic intestinal spirochetes of swine distinct from serpulina innocens isolate b256.	comparative analyses of a group of 16 weakly beta-hemolytic spirochetes isolated from feces and mucosal scrapings of intestines of swine in the midwestern united states, and eastern canada revealed the existence of a phenotypically and genotypically related group of 7 isolates. although isolates in this group differed from all known reference isolates of intestinal spirochetes of swine, partial similarity was detected with s. joneseae isolate 16, a newly identified weakly beta-hemolytic intestin ...	1993	8296452
polymerase chain reaction for identification of human and porcine spirochaetes recovered from cases of intestinal spirochaetosis.	a polymerase chain reaction (pcr) amplification of 16s rdna was developed to identify spirochaetes recovered from cases of intestinal spirochaetosis in humans and pigs; these bacteria belong to a distinct genetic group of spirochaetes, with the proposed name 'anguillina coli'. the pcr incorporated a universal eubacterial 16s rdna sequencing primer (1492r), and a 21-base forward primer designed to include a nucleotide sequence specific for 'a. coli'. the pcr was used to correctly identify dna ext ...	1995	7875570
outer membrane-associated serine protease of intestinal spirochetes.	pathogenic intestinal spirochetes cause damage to the intestinal mucosa of humans and animals by an unknown mechanism. the purpose of this study was to assess the pathogenic intestinal spirochetes serpulina hyodysenteriae, serpulina pilosicoli, and brachyspira aalborgi and the non-pathogenic commensal intestinal spirochetes serpulina innocens and treponema succinifaciens for protease activity. a partially heat stable, subtilisin-like, serine protease was identified in the outer membrane of all s ...	1997	9297834
cloning and dna sequence analysis of an immunogenic glucose-galactose mglb lipoprotein homologue from brachyspira pilosicoli, the agent of colonic spirochetosis.	colonic spirochetosis (cs) is a newly emerging infectious disease of humans and animals caused by the pathogenic spirochete brachyspira (formerly serpulina) pilosicoli. the purpose of this study was to characterize an antigen that was recognized by antibodies present in sera of challenge-exposed pigs. the gene encoding the antigen was identified by screening a plasmid library of human b. pilosicoli strain sp16 (atcc 49776) genomic dna with hyperimmune and convalescent swine sera. the predicted a ...	2000	10899855
detection and quantification of oral treponemes in subgingival plaque by real-time pcr.	oral treponemes have been associated with periodontal diseases. we developed a highly sensitive and specific method to detect and quantify cultivable oral treponemes (treponema denticola, treponema vincentii, and treponema medium) in 50 subgingival plaque samples from 13 healthy subjects as well as 37 patients with periodontal diseases using real-time pcr assays with specific primers and a taqman probe for each 16s rrna sequence. the specificity for each assay was examined by using dna specimens ...	2002	12202575
complete genome sequence of treponema succinifaciens type strain (6091).	treponema succinifaciens cwyk and canale-parola 1981 is of interest because this strictly anaerobic, apathogenic member of the genus treponema oxidizes carbohydrates and couples the embden-meyerhof pathway via activity of a pyruvate-formate lyase to the production of acetyl-coenzyme a and formate. this feature separates this species from most other anaerobic spirochetes. the genome of t. succinifaciens 6091(t) is only the second completed and published type strain genome from the genus treponema ...	2011	21886863
a de bruijn graph approach to the quantification of closely-related genomes in a microbial community.	the wide applications of next-generation sequencing (ngs) technologies in metagenomics have raised many computational challenges. one of the essential problems in metagenomics is to estimate the taxonomic composition of a microbial community, which can be approached by mapping shotgun reads acquired from the community to previously characterized microbial genomes followed by quantity profiling of these species based on the number of mapped reads. this procedure, however, is not as trivial as it ...	2012	22697249
identification and classification of bacterial type iii toxin-antitoxin systems encoded in chromosomal and plasmid genomes.	toxin-antitoxin systems are widespread in bacteria and archaea. they perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. toxin-antitoxin systems have been divided into three types, depending on the nature of the interacting macromolecules. the recently discovered type iii toxin-antitoxin systems encode protein toxins that are inhibited by pseudoknots of antitoxic rna, encoded by short ...	2012	22434880
restriction and sequence alterations affect dna uptake sequence-dependent transformation in neisseria meningitidis.	transformation is a complex process that involves several interactions from the binding and uptake of naked dna to homologous recombination. some actions affect transformation favourably whereas others act to limit it. here, meticulous manipulation of a single type of transforming dna allowed for quantifying the impact of three different mediators of meningococcal transformation: nlaiv restriction, homologous recombination and the dna uptake sequence (dus). in the wildtype, an inverse relationsh ...	2012	22768309
a phylogenomic and molecular signature based approach for characterization of the phylum spirochaetes and its major clades: proposal for a taxonomic revision of the phylum.	the spirochaetes species cause many important diseases including syphilis and lyme disease. except for their containing a distinctive endoflagella, no other molecular or biochemical characteristics are presently known that are specific for either all spirochaetes or its different families. we report detailed comparative and phylogenomic analyses of protein sequences from spirochaetes genomes to understand their evolutionary relationships and to identify molecular signatures for this group. these ...	2013	23908650
biochemical and molecular characterization of treponema phagedenis-like spirochetes isolated from a bovine digital dermatitis lesion.	bovine papillomatous digital dermatitis (dd) is the leading cause of lameness in dairy cattle and represents a serious welfare and economic burden. found primarily in high production dairy cattle worldwide, dd is characterized by the development of an often painful red, raw ulcerative or papillomatous lesion frequently located near the interdigital cleft and above the bulbs of the heel. while the exact etiology is unknown, several spirochete species have been isolated from lesion material. four ...	2013	24304812
genome-wide relatedness of treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen treponema denticola.	treponema pedis and t. denticola are two genetically related species with different origins of isolation. treponema denticola is part of the human oral microbiota and is associated with periodontitis while t. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. although multiple treponema phylotypes may exist in ulcerative lesions in pigs, t. pedis appears to be a predominant spirochete in these lesions. treponema pedis can also be ...	2013	23977007
the tp0796 lipoprotein of treponema pallidum is a bimetal-dependent fad pyrophosphatase with a potential role in flavin homeostasis.	treponema pallidum, an obligate parasite of humans and the causative agent of syphilis, has evolved the capacity to exploit host-derived metabolites for its survival. flavin-containing compounds are essential cofactors that are required for metabolic processes in all living organisms, and riboflavin is a direct precursor of the cofactors fmn and fad. unlike many pathogenic bacteria, treponema pallidum cannot synthesize riboflavin; we recently described a flavin-uptake mechanism composed of an ab ...	2013	23447540
phylogenetic analysis of pbp genes in treponemes.	β-lactamases are the main cause of bacterial resistance to penicillin, cephalosporins, and related β-lactam compounds. the presence of the novel penicillin-binding protein (pbp) tp47 in treponema pallidum has been reported to be a well-known mechanism for turnover of b-lactam antibiotics. although, t. pallidum remains sensitive to penicillin, clinically significant resistance to macrolides has emerged in many developing countries. the genome sequence of t. pallidum has shown the presence of gene ...	2013	23330059
subsistence strategies in traditional societies distinguish gut microbiomes.	recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in peru and an urban-industrialized community from the us. we find that in addition to taxonomic and metabolic differences between urban and traditional lifestyl ...	2015	25807110
social networks predict gut microbiome composition in wild baboons.	social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. rates of interaction directly explained variation in the gut microbiome, even after controlling for ...	2015	25774601
uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness.	uncovering the phylogenetic composition of microbial community and the potential functional capacity of microbiome in different gut locations is of great importance to pig production. here we performed a comparative analysis of gut microbiota and metagenomics among jejunum, ileum and cecum in pigs with distinct fatness. 16s rrna gene sequencing revealed dramatic differences of microbial composition, diversity and species abundance between small intestine and cecum. clostridium and smb53 were enr ...	2016	27255518
gut microbiome and dietary patterns in different saudi populations and monkeys.	host genetics, environment, lifestyle and proximity between hosts strongly influence the composition of the gut microbiome. to investigate the association of dietary variables with the gut microbiota, we used 16s rdna sequencing to test the fecal microbiome of bedouins and urban saudis and we compared it to the gut microbiome of baboons living in close contact with bedouins and eating their leftovers. we also analyzed fermented dairy products commonly consumed by bedouins in order to investigate ...	2016	27578328
variations in the post-weaning human gut metagenome profile as result of bifidobacterium acquisition in the western microbiome.	studies of the gut microbiome variation among human populations revealed the existence of robust compositional and functional layouts matching the three subsistence strategies that describe a trajectory of changes across our recent evolutionary history: hunting and gathering, rural agriculture, and urban post-industrialized agriculture. in particular, beside the overall reduction of ecosystem diversity, the gut microbiome of western industrial populations is typically characterized by the loss o ...	2016	27462302