scholarly journals Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene Cassettes

2012 ◽  
Vol 78 (15) ◽  
pp. 5288-5296 ◽  
Author(s):  
Yu-Wei Wu ◽  
Mina Rho ◽  
Thomas G. Doak ◽  
Yuzhen Ye
Keyword(s):  
Microbial Communities ◽  
De Novo ◽  
Human Subjects ◽  
Human Microbiome ◽  
Metagenomic Data ◽  
De Bruijn Graph ◽  
Content Type ◽  
Gene Cassettes ◽  
Dental Diseases ◽  
Normal Human

ABSTRACTThe NIH Human Microbiome Project (HMP) has produced several hundred metagenomic data sets, allowing studies of the many functional elements in human-associated microbial communities. Here, we survey the distribution of oral spirochetes implicated in dental diseases in normal human individuals, using recombination sites associated with the chromosomal integron inTreponemagenomes, taking advantage of the multiple copies of the integron recombination sites (repeats) in the genomes, and using a targeted assembly approach that we have developed. We find that integron-containingTreponemaspecies are present in ∼80% of the normal human subjects included in the HMP. Further, we are able tode novoassemble the integron gene cassettes using our constrained assembly approach, which employs a unique application of the de Bruijn graph assembly information; most of these cassette genes were not assembled in whole-metagenome assemblies and could not be identified by mapping sequencing reads onto the known referenceTreponemagenomes due to the dynamic nature of integron gene cassettes. Our study significantly enriches the gene pool known to be carried byTreponemachromosomal integrons, totaling 826 (598 97% nonredundant) genes. We characterize the functions of these gene cassettes: many of these genes have unknown functions. The integron gene cassette arrays found in the human microbiome are extraordinarily dynamic, with different microbial communities sharing only a small number of common genes.

scholarly journals hypDas a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

2014 ◽  
Vol 80 (12) ◽  
pp. 3776-3782 ◽  
Author(s):  
Christian Beimgraben ◽  
Kirstin Gutekunst ◽  
Friederike Opitz ◽  
Jens Appel
Keyword(s):  
Microbial Communities ◽  
Surface Waters ◽  
Hydrogen Uptake ◽  
Metagenomic Data ◽  
Trace Gas ◽  
Sequence Motifs ◽  
Environmental Distribution ◽  
Content Type ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs

ABSTRACTHydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and foundhypDto be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respectivehypDgenes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly ofActinobacteria,Acidobacteria, andBurkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) ofBurkholderiales,Rhizobiales, andRhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) ofLegionellalesand cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010,http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.

scholarly journals Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans

2014 ◽  
Vol 53 (1) ◽  
pp. 15-21 ◽  
Author(s):  
Nicole E. Moore ◽  
Jing Wang ◽  
Joanne Hewitt ◽  
Dawn Croucher ◽  
Deborah A. Williamson ◽  
...  
Keyword(s):  
New Zealand ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Diagnostic Testing ◽  
Illumina Miseq ◽  
Metagenomic Analysis ◽  
Metagenomic Data ◽  
Unknown Etiology ◽  
Data Set ◽  
Content Type

The etiology of an outbreak of gastroenteritis in humans cannot always be determined, and ∼25% of outbreaks remain unsolved in New Zealand. It is hypothesized that novel viruses may account for a proportion of unsolved cases, and new unbiased high-throughput sequencing methods hold promise for their detection. Analysis of the fecal metagenome can reveal the presence of viruses, bacteria, and parasites which may have evaded routine diagnostic testing. Thirty-one fecal samples from 26 gastroenteritis outbreaks of unknown etiology occurring in New Zealand between 2011 and 2012 were selected forde novometagenomic analysis. A total data set of 193 million sequence reads of 150 bp in length was produced on an Illumina MiSeq. The metagenomic data set was searched for virus and parasite sequences, with no evidence of novel pathogens found. Eight viruses and one parasite were detected, each already known to be associated with gastroenteritis, including adenovirus, rotavirus, sapovirus, andDientamoeba fragilis. In addition, we also describe the first detection of human parechovirus 3 (HPeV3) in Australasia. Metagenomics may thus provide a useful audit tool when applied retrospectively to determine where routine diagnostic processes may have failed to detect a pathogen.

scholarly journals Postmortem succession of gut microbial communities in deceased human subjects

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3437 ◽  
Author(s):  
Jennifer M. DeBruyn ◽  
Kathleen A. Hauther
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Human Subjects ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Postmortem Changes ◽  
Rrna Gene ◽  
Human Gut ◽  
Decomposition Processes ◽  
Over Time

The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs =  − 0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.

scholarly journals Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

2012 ◽  
Vol 78 (17) ◽  
pp. 6309-6320 ◽  
Author(s):  
Joanne B. Emerson ◽  
Brian C. Thomas ◽  
Karen Andrade ◽  
Eric E. Allen ◽  
Karla B. Heidelberg ◽  
...  
Keyword(s):  
De Novo ◽  
Detection Threshold ◽  
Microbial Evolution ◽  
Metagenomic Data ◽  
Hypersaline Lake ◽  
Metagenomic Sequence ◽  
Content Type ◽  
Natural Systems ◽  
Metagenomic Assembly ◽  
Insight Into

ABSTRACTViruses of theBacteriaandArchaeaplay important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. Here, we createdde novoassemblies from 6.4 Gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline Lake Tyrrell (LT), Victoria, Australia. Through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-like entities (VLEs, which could be viruses or plasmids). We tracked these 35 populations across the eight samples and found that they are generally stable on the timescale of days and transient on the timescale of years, with some exceptions. Cross-detection of the 35 LT populations in three previously described haloviral metagenomes was limited to a few genes, and most previously sequenced haloviruses were not detected in our samples, though 3 were detected upon reducing our detection threshold from 90% to 75% nucleotide identity. Similar results were obtained when we applied our methods to haloviral metagenomic data previously reported from San Diego, CA: 10 contigs that we assembled from that system exhibited a variety of detection patterns on a timescale of weeks to 1 month but were generally not detected in LT. Our results suggest that most haloviral populations have a limited or, possibly, a temporally variable global distribution. This study provides high-resolution insight into viral biogeography and dynamics and it places “snapshot” viral metagenomes, collected at a single time and location, in context.

scholarly journals Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

2015 ◽  
Vol 82 (1) ◽  
pp. 255-267 ◽  
Author(s):  
William C. Nelson ◽  
Yukari Maezato ◽  
Yu-Wei Wu ◽  
Margaret F. Romine ◽  
Stephen R. Lindemann
Keyword(s):  
De Novo ◽  
Metagenomic Data ◽  
Species Variation ◽  
Metagenomic Sequencing ◽  
Interspecies Interactions ◽  
Sequence Coverage ◽  
Data Set ◽  
Content Type ◽  
Genome Reconstruction ◽  
Wide Range

ABSTRACTTo gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled thede novoreconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. TwoHalomonasspp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of theHalomonaspopulations, one of theRhodobacteraceaepopulations, and theRhizobialespopulation. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.

Observations on a Relationship between Steroid Metabolism and the Concentration of Plasma Fibrinogen

1963 ◽  
Vol 10 (02) ◽  
pp. 400-405 ◽  
Author(s):  
B. A Amundson ◽  
L. O Pilgeram
Keyword(s):  
Blood Coagulation ◽  
Methyl Ether ◽  
Broad Spectrum ◽  
Human Subjects ◽  
Plasma Fibrinogen ◽  
Steroid Metabolism ◽  
Specific Site ◽  
Chain Reaction ◽  
Normal Human ◽  
A Chain

SummaryEnovid (5 mg norethynodrel and 0.075 mg ethynylestradiol-3-methyl ether) therapy in young normal human subjects causes an increase in plasma fibrinogen of 32.4% (P >C 0.001). Consideration of this effect together with other effects of Enovid on the activity of specific blood coagulatory factors suggests that the steroids are exerting their effect at a specific site of the blood coagulation and/or fibrinolytic system. The broad spectrum of changes which are induced by the steroids may be attributed to a combination of a chain reaction and feed-back control.

Relationship Between Mepacrine-Labelled Dense Body Number, Platelet Capacity to Accumulate 14C-5-HT and Platelet Density in the Bernard-Soulier and Hermansky-Pudlak Syndromes

1979 ◽  
Vol 42 (02) ◽  
pp. 694-704 ◽  
Author(s):  
F Rendu ◽  
A T Nurden ◽  
M Lebret ◽  
J P Caen
Keyword(s):  
Dense Body ◽  
Human Subjects ◽  
Human Platelets ◽  
Dense Bodies ◽  
Storage Organelle ◽  
Hereditary Disorders ◽  
Labelling Procedure ◽  
Normal Human ◽  
Hermansky Pudlak Syndrome ◽  
Bernard Soulier Syndrome

SummaryWe have used the mepacrine-labelling procedure to measure the dense body (serotonin storage organelle) content of the platelets of 2 hereditary disorders where abnormalities in dense body number were suspected. The platelets were incubated with mepacrine and examined by fluorescence microscopy. A mean number of 5.4 ± 0.8 (SD) dense bodies per platelet was calculated from the data obtained using platelets isolated from 40 normal human subjects. In contrast the platelets of 2 patients with the Bernard-Soulier syndrome contained an average of 14 and 17 labelled granules. This increase was associated with a much greater capacity of the platelets to accumulate 14C-5-HT. The opposite result was obtained using the platelets from 2 patients with the Hermansky-Pudlak syndrome which contained few granules labelled by mepacrine and took up less 14C-5-HT than normal human platelets. Centrifugation of the patients’ platelets on discontinuous sucrose gradients showed that the platelets of the 2 Bemard-Soulier patients were much denser than normal whereas a high proportion of low density platelets was observed in the Hermansky-Pudlak syndrome. These results further define the platelet abnormalities in the two syndromes and suggest that dense body number may be one of the factors governing platelet density.

ADRENERGIC CONTROL MECHANISM FOR ACTH SECRETION IN MAN

1973 ◽  
Vol 74 (2) ◽  
pp. 263-270 ◽  
Author(s):  
Yoshikatsu Nakai ◽  
Hiroo Imura ◽  
Teruya Yoshimi ◽  
Shigeru Matsukura
Keyword(s):  
Intravenous Infusion ◽  
Human Subjects ◽  
Blocking Agent ◽  
Inhibitory Effect ◽  
Plasma Acth ◽  
Acth Secretion ◽  
Glucose Levels ◽  
Alpha Receptors ◽  
Normal Human ◽  
Adrenergic Blocking

ABSTRACT In order to determine if an adrenergic mechanism is involved in the secretion of corticotrophin (ACTH), the effect of adrenergic-blocking or -stimulating agent on plasma ACTH, cortisol and glucose levels was studied in normal human subjects. The intravenous infusion of methoxamine, an alpha adrenergic-stimulating agent, caused a rise in plasma ACTH and cortisol. This increase in plasma ACTH and cortisol was significantly inhibited by the simultaneous administration of phentolamine, an alpha adrenergic-blocking agent, in combination with methoxamine. The intravenous infusion of propranolol, a beta adrenergic-blocking agent, caused no significant change in plasma ACTH and cortisol, although it enhanced the plasma ACTH response to insulin-induced hypoglycaemia. On the other hand, alpha adrenergicblockade by intravenous infusion of phentolamine significantly suppressed the plasma ACTH response to insulin-induced hypoglycaemia. These studies suggest a stimulatory effect of alpha receptors and a possible inhibitory effect of beta receptors on ACTH secretion in man.

Specialized systems for the processing of mnemonic information within the primate frontal cortex

1996 ◽  
Vol 351 (1346) ◽  
pp. 1455-1462 ◽  
Keyword(s):  
Frontal Cortex ◽  
Specific Activity ◽  
Human Subjects ◽  
Long Term Memory ◽  
Executive Processing ◽  
Severe Impairment ◽  
Normal Human ◽  
Short And Long Term ◽  
Cortical Association Areas

The lateral frontal cortex is involved in various aspects of executive processing within short- and long-term memory. It is argued that the different parts of the lateral frontal cortex make distinct contributions to memory that differ in terms of the level of executive processing that is carried out in interaction with posterior cortical systems. According to this hypothesis, the mid-dorsolateral frontal cortex (areas 46 and 9) is a specialized system for the monitoring and manipulation of information within working memory, whereas the mid-ventrolateral frontal cortex (areas 47/12 and 45) is involved in the active retrieval of information from the posterior cortical association areas. Data are presented which support this two-level hypothesis that posits two distinct levels of interaction of the lateral frontal cortex with posterior cortical association areas. Functional activation studies with normal human subjects have demonstrated specific activity within the mid-dorsolateral region of the frontal cortex during the performance of tasks requiring monitoring of self-generated and externally generated sequences of responses. In the monkey, lesions restricted to this region of the frontal cortex yield a severe impairment in performance of the above tasks, this impairment appearing against a background of normal performance on several basic mnemonic tasks. By contrast, a more severe impairment follows damage to the mid-ventrolateral frontal region and functional activation studies have demonstrated specific changes in activity in this region in relation to the active retrieval of information from memory.

scholarly journals Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 86
Author(s):  
Erin M. Garcia ◽  
Myrna G. Serrano ◽  
Laahirie Edupuganti ◽  
David J. Edwards ◽  
Gregory A. Buck ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Distinct Species ◽  
Vaginal Swab ◽  
Metagenomic Data ◽  
Gardnerella Vaginalis ◽  
Vaginal Epithelial Cells ◽  
Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

Sign in / Sign up

Export Citation Format

Share Document