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PubMed2025

From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.

Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.

Humans↗
PubMed2003

Wide geographic distribution of bacteriophages that lyse the same indigenous freshwater isolate (Sphingomonas sp. strain B18).

An indigenous freshwater bacterium (Sphingomonas sp. strain B18) from Lake Plubetasee (Schleswig-Holstein, Germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. This bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. Phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction pattern. Some phages were widely distributed, while different types coexisted in the same sample. It was concluded that phages could be a major factor in shaping the structure of bacterial communities and maintaining a high bacterial diversity.

Bacteriophages↗
PubMed1988

Bacterial adhesion to intravenous cannulae: influence of implantation in the rabbit and of enzyme treatments.

Comparison was made of the adhesion of Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, Klebsiella aerogenes and Pseudomonas aeruginosa to six types of intravascular cannula material. Adhesion to materials removed from rabbit tissues did not differ significantly between types of material or between bacterial species. In contrast, major differences were found when unimplanted materials were examined; the overall rank order of adhesiveness of bacteria to unimplanted materials (S. epidermidis greater than P. aeruginosa greater than S. aureus much greater than K. aerogenes greater than E. coli) was highly significant (F = 13.0, P less than 0.0005), and although no single material was consistently least attractive to all micro-organisms, FEP-Teflon and PTFE-Teflon showed significantly lower overall affinity for bacteria than other materials (P less than 0.001); all species showed a significant preference for a silicone polymer (P less than 0.0005). The nature of the bacterial surface structures responsible for adhesion were investigated by the actions of pronase and mixed glycosidase, which produced significant respective decreases and increases in adhesion of staphylococci to unimplanted materials; their effects on the Gram-negative bacilli were less consistent.

Animals↗
PubMed2005

The impact of homologous recombination on the generation of diversity in bacteria.

The imprint of demographic and selective processes on bacterial population structure needs to be evaluated as deviation from the expectations of an appropriate null neutral model. We explore the impact of varying the population mutation and recombination rates theta and rho on ideal populations, using a recently developed model of neutral drift at multiple loci. This model may be fitted to experimental data to provide estimates of these parameters, and we do so for seven bacterial species (Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Helicobacter pylori, Burkholderia pseudomallei and Bacillus cereus), illustrating that bacterial species vary extensively in these fundamental parameters. Historically, the influence of recombination has often been estimated through its influence on the Index of Association I(A). We show that this may be relatively insensitive to changes in either mutation or recombination rates. It is known that biased sampling can lead to artificially high estimates of I(A). We therefore provide a method of precisely separating the effects of such bias and true linkage between alleles. We also demonstrate that by fitting the neutral model to experimental data, more informative and precise estimates of the relative roles of recombination and mutation may be obtained.

Bacteria↗
PubMed2004

ATR-FTIR spectroscopy studies of iron-sulfur protein and cytochrome c1 in the Rhodobacter capsulatus cytochrome bc1 complex.

Redox transitions in the Rhodobacter capsulatus cytochrome bc(1) complex were investigated by perfusion-induced attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy combined with synchronous visible spectroscopy, in both the wild type and a cytochrome c(1) point mutant, M183K, in which the midpoint potential of heme was lowered from the wild-type value of 320 mV to 60 mV. Overall redox difference spectra of the wild type and M183K mutant were essentially identical, indicating that the mutation did not cause any major structural perturbation. Spectra were compared with data on the bovine bc(1) complex, and tentative assignments of several bands could be made by comparison with available data on model compounds and crystallographic structures. The bacterial spectra showed contributions from ubiquinone that were much larger than in the bovine enzyme, arising from additional bound and adventitious ubiquinone. The M183K mutant enabled selective reduction of the iron-sulfur protein which in turn allowed the IR redox difference spectra of ISP and cytochrome c(1) to be deconvoluted at high signal/noise ratios, and features of these spectra are interpreted in light of structural and mechanistic information.

Cytochromes c1↗
PubMed2001

Sequence type analysis and recombinational tests (START).

UNLABELLED: The 32-bit Windows application START is implemented using Visual Basic and C(++) and performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. AVAILABILITY: START is available at http://outbreak.ceid.ox.ac.uk/software.htm. CONTACT: keith.jolley@ceid.ox.ac.uk

Databases, Nucleic Acid↗
PubMed2006

Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes.

We describe the cloning, overexpression, purification, characterization and crystal structure of chitinase G, a single-domain family 19 chitinase from the Gram-positive bacterium Streptomyces coelicolor A3(2). Although chitinase G was not capable of releasing 4-methylumbelliferyl from artificial chitooligosaccharide substrates, it was capable of degrading longer chitooligosaccharides at rates similar to those observed for other chitinases. The enzyme was also capable of degrading a colored colloidal chitin substrate (carboxymethyl-chitin-remazol-brilliant violet) and a small, presumably amorphous, subfraction of alpha-chitin and beta-chitin, but was not capable of degrading crystalline chitin completely. The crystal structures of chitinase G and a related Streptomyces chitinase, chitinase C [Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T & Nonaka T (2006) J Mol Biol358, 472-484], showed that these bacterial family 19 chitinases lack several loops that extend the substrate-binding grooves in family 19 chitinases from plants. In accordance with these structural features, detailed analysis of the degradation of chitooligosaccharides by chitinase G showed that the enzyme has only four subsites (- 2 to + 2), as opposed to six (- 3 to + 3) for plant enzymes. The most prominent structural difference leading to reduced size of the substrate-binding groove is the deletion of a 13-residue loop between the two putatively catalytic glutamates. The importance of these two residues for catalysis was confirmed by a site-directed mutagenesis study.

Amino Acid Sequence↗
PubMed1982

Comparisons between carcinogenic potency and mutagenic potency to Salmonella in a series of derivatives of 4-dimethylaminoazobenzene (DAB).

8 derivatives of the rodent liver carcinogen 4-dimethylaminoazobenzene (DAB), all of known carcinogenicity in rodents, have been evaluated in the 3 major variants of the Salmonella mutation assay; the standard plate test of Ames et al., the pre-incubation assay of Yahagi et al. and the fluctuation assay of Gatehouse. Although 4 of these chemicals were reported to be non-carcinogenic, and 4 to be of greater carcinogenic potency than DAB, each was mutagenic in a least 2 of the assays. Further, no quantitative correlation between carcinogenic and mutagenic potency was evident in any of the assay employed. The parent carcinogen DAB, 5-dimethylaminophenylazoindazole (a non-carcinogenic bacterial mutagen) and 6-dimethylaminophenylazobenzthiazole (a carcinogenic bacterial mutagen) were administered to rats via intraperitoneal injection, followed, 26 h later, by a sub-acute dose of [14C] dimethylnitrosamine. The histopathological condition of the livers of the treated animals was assessed together with a determination of the extent and nature of methylation by DMN of the DNA in the livers according to the method of O'Connor. Disturbances in both the pathological and DNA-related parameters were observed for the 2 carcinogens while control levels were seen for the non-carcinogen. Within this context the value of short-term assays conducted in vivo is discussed, especially their potential to identify potent mammalian carcinogens from among a collection of structurally related bacterial mutagens.

Animals↗
PubMed2004

Enterococcal cytolysin: activities and association with other virulence traits in a pathogenicity island.

Enterococcal cytolysin is a structurally novel bacterial toxin expressed by some strains of E. faecalis and is distantly related to the class of bacteriocins known as lantibiotics. The cytolysin can be encoded by large pheromone-responsive plasmids, or on the chromosome within pathogenicity island. It is produced by a complex process that involves the products of eight genes, designated cylR1, cylR2, cylLL, cylLS, cylM, cylB, cylA, and cylI. The cytolysin toxin, maturation and regulatory genes are organized into two divergent transcripts: a structural transcript cylLLLSMBAI, and a regulatory transcript cylR1R2. The active cytolysin subunits, CylLL" and CylLS", are synthesized ribosomally as non-identical peptides, post-translationally modified, then secreted and activated. The cytolysin operon is repressed by the activities of two proteins, CylR1 and CylR2, and derepressed by a quorum-sensing process involving secreted autoinducer CylLS". The cytolysin operon within the E. faecalis pathogenicity island is associated with other virulence determinants, including aggregation substance and enterococcal surface protein, Esp.

Bacterial Proteins↗
PubMed2000

Chemical, physical and enzymatic pre-treatments of probiotic lactobacilli alter their adhesion to human intestinal mucus glycoproteins.

Intestinal mucus glycoproteins extracted from faeces of healthy adult subjects were used as a substratum for bacterial adhesion to investigate the effects of physical, chemical and enzymatic pre-treatments of the bacteria on their adhesion. The strains studied were Lactobacillus acidophilus 1 (LCI, Nestlé), L. rhamnosus strain GG (ATCC 53103), L. rhamnosus LC-705, and L. casei strain Shirota (Yakult, Yakult Ltd). Hereafter the strains are referred to as LA1, LGG, LC-705, and Shirota, respectively. Strains LA1 and LGG adhered greatly whereas the adhesion of strains LC-705 and Shirota to intestinal mucus glycoproteins was low. Adhesion of LA1 and LGG was reduced by boiling, autoclaving and by pepsin and trypsin treatments suggesting that the bacterial protein structures are essential for their adhesion. Treatment in ethanol and in propanol prior to adhesion significantly increased the adhesion of LA1 and LC-705, respectively. Adhesion of Shirota strain was not altered by any of the treatments.

Bacterial Adhesion↗
PubMed1997

Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.3 A structure of an aspartate to lysine mutant at position 13 of CheY.

An aspartate to lysine mutation at position 13 of the chemotaxis regulatory protein CheY causes a constitutive tumbly phenotype when expressed at high copy number in vivo even though the mutant protein is not phosphorylatable. These properties suggest that the D13K mutant adopts the active, signaling conformation of CheY independent of phosphorylation, so knowledge of its structure could explain the activation mechanism of CheY. The x-ray crystallographic structure of the CheY D13K mutant has been solved and refined at 2.3 A resolution to an R-factor of 14.3%. The mutant molecule shows no significant differences in backbone conformation when compared with the wild-type, Mg2+-free structure, but there are localized changes within the active site. The side chain of lysine 13 blocks access to the active site, whereas its epsilon-amino group has no bonding interactions with other groups in the region. Also in the active site, the bond between lysine 109 and aspartate 57 is weakened, and the solvent structure is perturbed. Although the D13K mutant has the inactive conformation in the crystalline form, rearrangements in the active site appear to weaken the overall structure of that region, potentially creating a metastable state of the molecule. If a conformational change is required for signaling by CheY D13K, then it most likely proceeds dynamically, in solution.

Amino Acid Sequence↗
PubMed1986

[Bacterial antigenic polysaccharides. 20. The structure of the O-specific polysaccharide chain of Pseudomonas aeruginosa O(3a),3d,3f (Lányi) lipopolysaccharide].

Mild acid degradation of lipopolysaccharide from Pseudomonas aeruginosa O(3a), 3d, 3f (Lányi classification) afforded O-specific polysaccharide containing N-acetyl-D-fucosamine, 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid, 3-acetamidino-2-acetamido-2,3-dideoxy-L-guluronic and D-mannuronic acid as well as O-acetyl groups. On the basis of O-deacetylation, selective cleavage with anhydrous fluoride, chemical transformation of the oligosaccharides obtained (hydrolysis or reductive deamination of the acetamidino group into acetamido or ethylamino group, respectively) and analysis by 13C NMR spectroscopy, it was concluded that the polysaccharide is built up mainly by trisaccharide repeating units of types A and B in the ratio approximately 2:1: (Formula: see text). The units of both types most probably enter the same polymeric chain. If so, such a hybrid structure can be accounted for by incompleteness of epimerization at C5 of the acetamidino derivative of mannuronic acid at the polymer level in the course of biosynthesis of this polysaccharide.

Antigens, Bacterial↗
PubMed1995

Three-dimensional model of the alpha-subunit of bacterial luciferase.

The predicted secondary structure of both subunits of bacterial luciferase is in accordance with a regular 8-fold alpha/beta-barrel structure. The 3D profile confirmed that luciferase subunits are compatible with the alpha/beta-barrel despite the absence of sequence similarity with any alpha/beta-barrel protein. The three-dimensional structure of 260 residues of the alpha-chain of luciferase was modeled from coordinates of glycolate oxidase and then energy minimized. The model obtained satisfies the criteria for the structure of a globular protein and is in accordance with known experimental data. From the model it is possible to predict active site residues involved in binding and catalysis. These predictions, and thus also the model, can be tested by protein engineering experiments.

Aldehydes↗
PubMed1991

Protein-kinase-C-independent activation of arachidonate release and prostaglandin E2 formation in macrophages interacting with certain bacteria.

Certain bacterial species, of which we selected Fusobacterium nucleatum, Gardnerella vaginalis, Peptostreptococcus anaerobius and Propionibacterium acnes, were found to induce release of arachidonic acid in a dose- and time-dependent manner in mouse macrophages. The release of arachidonic acid showed a characteristic lag period of approximately 10 min and was accompanied by selective transformation into prostaglandin E2. Bacteria killed by various methods caused a similar response, indicating that bacterial surface structures rather than secreted products were involved. Down-regulation of protein kinase C by treatment of macrophages with 4 beta-phorbol 12-myristate 13-acetate hardly affected the response to bacteria at all, except for a partial inhibition in the case of P. acnes. Furthermore, the generation of prostaglandin E2 was synergistically enhanced when macrophages were exposed to both bacteria and phorbol ester. It is also unlikely that bacterial activation was mediated exclusively via a rise in cytosolic [Ca2+], since bacteria stimulated the release of arachidonic acid also when [Ca2+] was clamped at various levels and since the response to bacteria was enhanced in an additive to synergistic manner when combined with calcium ionophore. Changes in protein phosphorylation in macrophages exposed to F. nucleatum (Gram-negative) were virtually identical to those seen with bacterial lipopolysaccharide, while P. anaerobius (Gram-positive) induced enhanced labeling of a single detectable phosphoprotein. In both cases, the changes in protein phosphorylation showed a time lag of 4-8 min and occurred independently of protein kinase C, consistent with a possible role in signal transduction. These results demonstrate that certain bacteria cause activation of arachidonic acid release and prostaglandin E2 formation in mouse macrophages; that the response is independent of protein kinase C and that it is not wholly mediated via a rise in cytosolic [Ca2+].

Animals↗
PubMed2005

Bacterial biofilm within diseased pancreatic and biliary tracts.

BACKGROUND: Bacterial community structures in human pancreatic and biliary tracts were evaluated. METHODS: Gall bladder stones from 153 patients, 20 gall bladder walls, six common duct stones, 52 biliary stents, 21 duodenal biopsies, nine pancreatic duct biopsies, and five bile ducts were investigated using fluorescence in situ hybridisation (FISH) with ribosomal RNA targeted Cy3/Cy5 (carbocyanine) labelled oligonucleotide probes. RESULT: Duodenal, gall bladder, and bile duct walls were free of bacteria. A dense multispecies bacterial biofilm was present within the pancreatic duct of patients with calcific pancreatitis and within biliary stents, irrespective of diagnosis. The concentration, density, and amenability of the biofilm to FISH and DNA staining declined progressively with the grade of stent occlusion. The lowest detectable bacterial concentrations were found by FISH in completely occluded stents and brown/mixed gall stones. Bacteria were not detectable with FISH in cholesterol gall stones. CONCLUSIONS: A wide range of different branches and groups of bacteria participate in the development of biofilms on the surfaces of foreign bodies, such as biliary stents, mixed gall stones, or calcific pancreatic ducts, but not on the surface of pure cholesterol gall stones. Occlusion of stents leads to progressive extinction of the biofilm and mummification of its components. Deposition of cholesterol or other substances within the biofilm matrix may be a novel mechanism of host defence against bacteria present in these biofilms.

Bacteria↗
PubMed2006

The effects of water treatment residues on soil respiration and microbial community structure.

Land disposal of water treatment residue (WTR), a by-product of potable water production, is increasingly being considered a viable alternative to land filling. It is crucial, inter alia, that soil quality is not affected adversely. Six different WTRs obtained from South African water treatment facilities were added to Hutton and Westleigh topsoils at rates of 0, 5, 15 and 25% (m/m) to determine their impacts on soil basal respiration. In general, respiration increased with rate of addition of WTR. The Umgeni, Rand, Midvaal and Faure2 WTRs had the greatest effect on respiration. Increases in respiration became less marked with time. The Hutton topsoil was mixed with the WTRs (at 15% m/m) and, following incubation, the bacterial community structure was examined by denaturing gradient gel electrophoresis. Changes in community structure were detected after 5 d and were attributed to physico-chemical changes arising from WTR amendment. However, dominant bands associated with the Hutton soil were retained and microbial diversity was not adversely affected. The findings of this investigation suggest that WTRs can be applied to the Hutton soil at a rate of at least 15% (300 Mg ha(-1)) without having a detrimental effect on microbial indicators of soil quality.

Hydrogen-Ion Concentration↗
PubMed2003

Diversity and succession of the intestinal bacterial community of the maturing broiler chicken.

The diversity of bacterial floras in the ilea and ceca of chickens that were fed a vegetarian corn-soy broiler diet devoid of feed additives was examined by analysis of 1,230 partial 16S rRNA gene sequences. Nearly 70% of sequences from the ileum were related to those of Lactobacillus, with the majority of the rest being related to Clostridiaceae (11%), Streptococcus (6.5%), and Enterococcus (6.5%). In contrast, Clostridiaceae-related sequences (65%) were the most abundant group detected in the cecum, with the other most abundant sequences being related to Fusobacterium (14%), Lactobacillus (8%), and Bacteroides (5%). Statistical analysis comparing the compositions of the different 16S rRNA libraries revealed that population succession occurred during some sampling periods. The significant differences among cecal libraries at 3 and 7 days of age, at 14 to 28 days of age, and at 49 days of age indicated that successions occurred from a transient community to one of increasing complexity as the birds aged. Similarly, the ileum had a stable bacterial community structure for birds at 7 to 21 days of age and between 21 to 28 days of age, but there was a very unique community structure at 3 and 49 days of age. It was also revealed that the composition of the ileal and cecal libraries did not significantly differ when the birds were 3 days old, and in fact during the first 14 days of age, the cecal microflora was a subset of the ileal microflora. After this time, the ileum and cecum had significantly different library compositions, suggesting that each region developed its own unique bacterial community as the bird matured.

Animal Feed↗
PubMed1995

Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.1-A structure of a threonine to isoleucine mutant at position 87 of CheY.

Position 87 of the chemotaxis regulatory protein CheY is a highly conserved threonine/serine residue in the response regulator superfamily. A threonine 87 to isoleucine mutant in CheY, identified by its in vivo non-chemotactic phenotype, was also found to be phosphorylatable in vitro. These properties indicate that this mutant does not undergo activation upon phosphorylation. The x-ray crystallographic structure of the threonine to isoleucine CheY mutant has been solved and refined at 2.1-A resolution, to an R factor of 15.6%. Comparison with the wild-type, Mg(2+)-free CheY structure shows that the active site structure is retained, but there are significant localized differences in the backbone conformation distal from the substitution. The presence of the isoleucine side chain also restricts the rotational conformation of another conserved residue in the molecule, tyrosine at position 106. These results provide further evidence for a signaling surface remote from the phosphorylation site of the CheY molecule and implicate threonine 87 and other residues in the post-phosphorylation signaling events.

Bacterial Proteins↗