scholarly journals Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse

2015 ◽  
Vol 83 (11) ◽  
pp. 4383-4391 ◽  
Author(s):  
Ekaterina G. Semenyuk ◽  
Valeriy A. Poroyko ◽  
Pehga F. Johnston ◽  
Sara E. Jones ◽  
Katherine L. Knight ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Content ◽  
Rrna Gene ◽  
Gi Tract ◽  
Bacterial Populations ◽  
Content Type ◽  
Minority Member ◽  
Gene Sequence Analysis

ABSTRACTClostridium difficileinfection (CDI) is a major cause of health care-associated disease. CDI initiates with ingestion ofC. difficilespores, germination in the gastrointestinal (GI) tract, and then colonization of the large intestine. The interactions betweenC. difficilecells and other bacteria and with host mucosa during CDI remain poorly understood. Here, we addressed the hypothesis that, in a mouse model of CDI,C. difficileresides in multicellular communities (biofilms) in association with host mucosa. To do this, we paraffin embedded and then sectioned the GI tracts of infected mice at various days postinfection (p.i.). We then used fluorescentin situhybridization (FISH) with 16S rRNA probes targeting most bacteria as well asC. difficilespecifically. The results revealed thatC. difficileis present as a minority member of communities in the outer (loose) mucus layer, in the cecum and colon, starting at day 1 p.i. To generate FISH probes that identify bacteria within mucus-associated communities harboringC. difficile, we characterized bacterial populations in the infected mouse GI tract using 16S rRNA gene sequence analysis of bacterial DNA prepared from intestinal content. This analysis revealed the presence of genera of several families belonging toBacteroidetesandFirmicutes. These data suggest that formation of multispecies communities associated with the mucus of the cecum and colon is an important early step in GI tract colonization. They raise the possibility that other bacterial species in these communities modulate the ability ofC. difficileto successfully colonize and, thereby, cause disease.

scholarly journals Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3862-3866 ◽  
Author(s):  
Shi Peng ◽  
Dong Dan Hong ◽  
Yang Bing Xin ◽  
Li Ming Jun ◽  
Wei Ge Hong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1T showed 96.8 % similarity to Sphingobacterium nematocida CCTCC AB 2010390T and less than 95.2 % similarity to other members of the genus Sphingobacterium . Growth of strain CCNWSP36-1T occurred at 10–40 °C and at pH 5.0–9.0. The NaCl range (w/v) for growth was 0–4 %. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1T ( = ACCC 19328T = JCM 30166T).

scholarly journals Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

2012 ◽  
Vol 78 (7) ◽  
pp. 2359-2366 ◽  
Author(s):  
Merritt G. Gillilland ◽  
John R. Erb-Downward ◽  
Christine M. Bassis ◽  
Michael C. Shen ◽  
Galen B. Toews ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Structural Heterogeneity ◽  
Ecological Succession ◽  
Rrna Gene ◽  
Gi Tract ◽  
Content Type ◽  
Germ Free ◽  
Over Time

ABSTRACTLittle is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by eitherEscherichiaorBacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a “pioneering” community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.

scholarly journals Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3235-3239 ◽  
Author(s):  
Wan-Hoe Kim ◽  
Siwon Lee ◽  
Tae-Young Ahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Taxonomic Approach ◽  
Shallow Stream

A Gram-reaction-positive, rod-shaped, strictly aerobic and non-motile bacterial strain, designated WS16T, was isolated from the sediment of a shallow stream located in Cheonan, Korea. The strain grew optimally at 28 °C, at pH 7.0 and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequences suggested that the isolate belonged to the genus Flavihumibacter of the phylum Bacteroidetes . Comparative 16S rRNA gene sequence analysis showed that strain WS16T was related most closely to Flavihumibacter petaseus T41T (96.8 % similarity). The isolate contained MK-7 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH as the major fatty acids. The genomic DNA G+C content of the isolate was 45.9 mol%. The results of a polyphasic taxonomic approach indicated that strain WS16T represents a novel species of the genus Flavihumibacter , for which the name Flavihumibacter cheonanensis sp. nov. is proposed. The type strain is WS16T ( = KACC 17467T = JCM 19322T).

scholarly journals Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

2013 ◽  
Vol 80 (2) ◽  
pp. 478-485 ◽  
Author(s):  
Yue Tang ◽  
Anthony Underwood ◽  
Adriana Gielbert ◽  
Martin J. Woodward ◽  
Liljana Petrovska
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Abundant Species ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Content Type ◽  
Chicken Gut Microbiota

ABSTRACTThe animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identifiedClostridiales,Bacteroidaceae, andLactobacillaceaespecies as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged toLactobacillusspp., 155 belonged toClostridiumspp., and 66 belonged toStreptococcusspp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

scholarly journals Taxonomic revision of the genus Geobacillus : emendation of Geobacillus , G. stearothermophilus , G. jurassicus , G. toebii , G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly ‘thermoglucosidasius’); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov.

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1470-1485 ◽  
Author(s):  
An Coorevits ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Liesbeth Lebbe ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA–DNA hybridization experiments. Distinct clusters of the species Geobacillus stearothermophilus , Geobacillus thermodenitrificans , Geobacillus toebii and Geobacillus thermoglucosidasius were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species Geobacillus jurassicus , Geobacillus subterraneus and Geobacillus caldoxylosilyticus was confirmed. It is proposed that the name Geobacillus thermoglucosidasius be corrected to Geobacillus thermoglucosidans nom. corrig. Bacillus thermantarcticus clustered between Geobacillus species on the basis of 16S rRNA gene sequence analysis, and its transfer to the genus Geobacillus as Geobacillus thermantarcticus comb. nov. (type strain LMG 23032T = DSM 9572T = strain M1T = R-35644T) is proposed. The above-mentioned species, together with Geobacillus thermoleovorans and Geobacillus thermocatenulatus , form a monophyletic cluster representing the genus Geobacillus . The distinctiveness of ‘Geobacillus caldoproteolyticus’ was confirmed and it is proposed that it be accommodated, along with Geobacillus tepidamans , in the genus Anoxybacillus as Anoxybacillus caldiproteolyticus sp. nov. (type strain DSM 15730T = ATCC BAA-818T = LMG 26209T = R-35652T) and Anoxybacillus tepidamans comb. nov. (type strain LMG 26208T = ATCC BAA-942T = DSM 16325T = R-35643T), respectively. The type strain of Geobacillus debilis was not closely related to any members of the genera Anoxybacillus and Geobacillus , and it is proposed that this species be placed in the new genus Caldibacillus as Caldibacillus debilis gen. nov. comb. nov. The type strain of the type species, Caldibacillus debilis, is LMG 23386T ( = DSM 16016T = NCIMB 13995T = TfT = R-35653T).

scholarly journals Toward an Understanding of Changes in Diversity Associated with Fecal Microbiome Transplantation Based on 16S rRNA Gene Deep Sequencing

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Dea Shahinas ◽  
Michael Silverman ◽  
Taylor Sittler ◽  
Charles Chiu ◽  
Peter Kim ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Deep Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
Content Type ◽  
Fecal Microbiome ◽  
Level Analysis

ABSTRACT Fecal microbiome transplantation by low-volume enema is an effective, safe, and inexpensive alternative to antibiotic therapy for patients with chronic relapsing Clostridium difficile infection (CDI). We explored the microbial diversity of pre- and posttransplant stool specimens from CDI patients (n = 6) using deep sequencing of the 16S rRNA gene. While interindividual variability in microbiota change occurs with fecal transplantation and vancomycin exposure, in this pilot study we note that clinical cure of CDI is associated with an increase in diversity and richness. Genus- and species-level analysis may reveal a cocktail of microorganisms or products thereof that will ultimately be used as a probiotic to treat CDI. IMPORTANCE Antibiotic-associated diarrhea (AAD) due to Clostridium difficile is a widespread phenomenon in hospitals today. Despite the use of antibiotics, up to 30% of patients are unable to clear the infection and suffer recurrent bouts of diarrheal disease. As a result, clinicians have resorted to fecal microbiome transplantation (FT). Donor stool for this type of therapy is typically obtained from a spouse or close relative and thoroughly tested for various pathogenic microorganisms prior to infusion. Anecdotal reports suggest a very high success rate of FT in patients who fail antibiotic treatment (>90%). We used deep-sequencing technology to explore the human microbial diversity in patients with Clostridium difficile infection (CDI) disease after FT. Genus- and species-level analysis revealed a cocktail of microorganisms in the Bacteroidetes and Firmicutes phyla that may ultimately be used as a probiotic to treat CDI.

Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1126-1131 ◽  
Author(s):  
M. Madhaiyan ◽  
S. Poonguzhali ◽  
V. S. Saravanan ◽  
K. Hari ◽  
K.-C. Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Two strains, designated Sac-22T and Sac-41T, were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Betaproteobacteria , their closest relatives being Pseudoduganella violaceinigra and Duganella zoogloeoides with 16S rRNA gene sequence pairwise similarities of 96.4–97.2 % to the two novel strains. Strains Sac-22T and Sac-41T shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22T and 54.9 mol% for strain Sac-41T. Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22T and Sac-41T from all recognized species of the genus Duganella , it was concluded that strains represent two novel species in the genus Duganella for which the names Duganella sacchari sp. nov. (type strain Sac-22T = KCTC 22381T = NCIMB 14475T) and Duganella radicis sp. nov. (type strain Sac-41T = KCTC 22382T = NCIMB 14476T) are proposed.

scholarly journals Microbacterium sediminis sp. nov., a psychrotolerant, thermotolerant, halotolerant and alkalitolerant actinomycete isolated from deep-sea sediment

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 25-30 ◽  
Author(s):  
Libo Yu ◽  
Qiliang Lai ◽  
Zhiwei Yi ◽  
Limin Zhang ◽  
Ying Huang ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

An aerobic, rod-shaped, Gram-positive, oxidase- and catalase-positive bacterial isolate, strain YLB-01T, was characterized using phenotypic and molecular taxonomic methods. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Microbacterium and represented an evolutionary lineage that was distinct from recognized species of the genus Microbacterium . The isolate showed <97 % 16S rRNA gene sequence similarity with respect to the type strains of all of the members of the genus Microbacterium with validly published names. Cell-wall hydrolysate from the isolate contained the amino acids ornithine, alanine, glycine homoserine and glutamic acid, and the cell-wall sugars consisted of ribose, glucose and galactose. The main respiratory quinones were MK-8, 9, 10 and 11. The major cellular fatty acids were anteiso-C15 : 0 (38.5 %), anteiso-C17 : 0 (23.1 %) and C16 : 0 (18.9 %). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. The DNA G+C content of strain YLB-01T was 71 mol%. On the basis of the morphological, physiological and chemotaxonomic data and the results of comparative 16S rRNA gene sequence analysis, this isolate represents a novel species of the genus Microbacterium , for which the name Microbacterium sediminis sp. nov. is proposed. The type strain is YLB-01T ( = DSM 23767T = CCTCC AB2010363T = MCCC 1A06153T).

scholarly journals Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

2011 ◽  
Vol 78 (2) ◽  
pp. 511-518 ◽  
Author(s):  
Yohei Watanabe ◽  
Fumiko Nagai ◽  
Masami Morotomi
Keyword(s):  
Bacterial Species ◽  
Short Chain Fatty Acids ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Gi Tract ◽  
Bacterial Strains ◽  
High Sequence Identity ◽  
Healthy Human ◽  
Content Type

ABSTRACTIsolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067Tand YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related toPhascolarctobacterium faeciumACM 3679T, with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacteriumParaprevotella xylaniphilaYIT 11841T, in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067T. Real-time PCR analysis also revealed that YIT 12067T-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 108cells/g feces. These results indicate that YIT 12067T-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067Tand YIT 12068 suggest that these strains represent a novel species, which we have designatedPhascolarctobacterium succinatutenssp. nov.

scholarly journals Microbiome Data Distinguish Patients with Clostridium difficile Infection and Non-C. difficile-Associated Diarrhea from Healthy Controls

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Alyxandria M. Schubert ◽  
Mary A. M. Rogers ◽  
Cathrin Ring ◽  
Jill Mogle ◽  
Joseph P. Petrosino ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Colonization Resistance ◽  
Bacterial Populations ◽  
Content Type ◽  
Increased Risk ◽  
Community Types ◽  
Microbiome Data

ABSTRACTAntibiotic usage is the most commonly cited risk factor for hospital-acquiredClostridium difficileinfections (CDI). The increased risk is due to disruption of the indigenous microbiome and a subsequent decrease in colonization resistance by the perturbed bacterial community; however, the specific changes in the microbiome that lead to increased risk are poorly understood. We developed statistical models that incorporated microbiome data with clinical and demographic data to better understand why individuals develop CDI. The 16S rRNA genes were sequenced from the feces of 338 individuals, including cases, diarrheal controls, and nondiarrheal controls. We modeled CDI and diarrheal status using multiple clinical variables, including age, antibiotic use, antacid use, and other known risk factors using logit regression. This base model was compared to models that incorporated microbiome data, using diversity metrics, community types, or specific bacterial populations, to identify characteristics of the microbiome associated with CDI susceptibility or resistance. The addition of microbiome data significantly improved our ability to distinguish CDI status when comparing cases or diarrheal controls to nondiarrheal controls. However, only when we assigned samples to community types was it possible to differentiate cases from diarrheal controls. Several bacterial species within theRuminococcaceae,Lachnospiraceae,Bacteroides, andPorphyromonadaceaewere largely absent in cases and highly associated with nondiarrheal controls. The improved discriminatory ability of our microbiome-based models confirms the theory that factors affecting the microbiome influence CDI.IMPORTANCEThe gut microbiome, composed of the trillions of bacteria residing in the gastrointestinal tract, is responsible for a number of critical functions within the host. These include digestion, immune system stimulation, and colonization resistance. The microbiome’s role in colonization resistance, which is the ability to prevent and limit pathogen colonization and growth, is key for protection againstClostridium difficileinfections. However, the bacteria that are important for colonization resistance have not yet been elucidated. Using statistical modeling techniques and different representations of the microbiome, we demonstrated that several community types and the loss of several bacterial populations, includingBacteroides,Lachnospiraceae, andRuminococcaceae, are associated with CDI. Our results emphasize the importance of considering the microbiome in mediating colonization resistance and may also direct the design of future multispecies probiotic therapies.

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