scholarly journals Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

mBio ◽  
2014 ◽  
Vol 5 (5) ◽  
Author(s):  
Alexander Zaborin ◽  
Daniel Smith ◽  
Kevin Garfield ◽  
John Quensen ◽  
Baddr Shakhsheer ◽  
...  
Keyword(s):  
Critical Illness ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Multidrug Resistant ◽  
Nutrient Deprivation ◽  
Local Conditions ◽  
16S Rrna Analysis ◽  
Prolonged Stay ◽  
Content Type ◽  
Low Diversity

ABSTRACT We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style. IMPORTANCE During critical illness, the normal gut microbiota becomes disrupted in response to host physiologic stress and antibiotic treatment. Here we demonstrate that the community structure of the gut microbiota during prolonged critical illness is dramatically changed such that in many cases only two-member pathogen communities remain. Most of these ultra-low-membership communities display low virulence when grouped together (i.e., a commensal lifestyle); individually, however, they can express highly harmful behaviors (i.e., a pathogenic lifestyle). The commensal lifestyle of the whole community can be shifted to a pathogenic one in response to host factors such as opioids that are released during physiologic stress and critical illness. This shift can be prevented by using compounds such as Pi-PEG15-20 that interrupt bacterial virulence expression. Taking the data together, this report characterizes the plasticity seen with respect to the choice between a commensal lifestyle and a pathogenic lifestyle among ultra-low-diversity pathogen communities that predominate in the gut during critical illness and offers novel strategies for prevention of sepsis.

scholarly journals ArmA Methyltransferase in a Monophasic Salmonella enterica Isolate from Food

2011 ◽  
Vol 55 (11) ◽  
pp. 5262-5266 ◽  
Author(s):  
Sophie A. Granier ◽  
Laura Hidalgo ◽  
Alvaro San Millan ◽  
Jose Antonio Escudero ◽  
Belen Gutierrez ◽  
...  
Keyword(s):  
16S Rrna ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Broad Host Range ◽  
En Bloc ◽  
Content Type ◽  
Route Of Transmission ◽  
Amoxicillin Clavulanate ◽  
High Level ◽  
Level Resistance

ABSTRACTThe 16S rRNA methyltransferase ArmA is a worldwide emerging determinant that confers high-level resistance to most clinically relevant aminoglycosides. We report here the identification and characterization of a multidrug-resistantSalmonella entericasubspecies I.4,12:i:− isolate recovered from chicken meat sampled in a supermarket on February 2009 in La Reunion, a French island in the Indian Ocean. Susceptibility testing showed an unusually high-level resistance to gentamicin, as well as to ampicillin, expanded-spectrum cephalosporins and amoxicillin-clavulanate. Molecular analysis of the 16S rRNA methyltransferases revealed presence of thearmAgene, together withblaTEM-1,blaCMY-2, andblaCTX-M-3. All of these genes could be transferreden blocthrough conjugation intoEscherichia coliat a frequency of 10−5CFU/donor. Replicon typing and S1 pulsed-field gel electrophoresis revealed that thearmAgene was borne on an ∼150-kb broad-host-range IncP plasmid, pB1010. To elucidate howarmAhad integrated in pB1010, a PCR mapping strategy was developed for Tn1548, the genetic platform forarmA.The gene was embedded in a Tn1548-like structure, albeit with a deletion of the macrolide resistance genes, and an IS26was inserted within themelgene. To our knowledge, this is the first report of ArmA methyltransferase in food, showing a novel route of transmission for this resistance determinant. Further surveillance in food-borne bacteria will be crucial to determine the role of food in the spread of 16S rRNA methyltransferase genes worldwide.

scholarly journals Ecological Divergence of a Novel Group of Chloroflexus Strains along a Geothermal Gradient

2012 ◽  
Vol 79 (4) ◽  
pp. 1353-1358 ◽  
Author(s):  
Michael L. Weltzer ◽  
Scott R. Miller
Keyword(s):  
16S Rrna ◽  
Carbon Fixation ◽  
Hot Spring ◽  
Environmental Gradients ◽  
Geothermal Gradient ◽  
Geothermal Systems ◽  
Local Conditions ◽  
Content Type ◽  
Thermal Niche ◽  
Coa Reductase

ABSTRACTEnvironmental gradients are expected to promote the diversification and coexistence of ecological specialists adapted to local conditions. Consistent with this view, genera of phototrophic microorganisms in alkaline geothermal systems generally appear to consist of anciently divergent populations which have specialized on different temperature habitats. At White Creek (Lower Geyser Basin, Yellowstone National Park), however, a novel, 16S rRNA-defined lineage of the filamentous anoxygenic phototrophChloroflexus(OTU 10, phylumChloroflexi) occupies a much wider thermal niche than other 16S rRNA-defined groups of phototrophic bacteria. This suggests thatChloroflexusOTU 10 is either an ecological generalist or, alternatively, a group of cryptic thermal specialists which have recently diverged. To distinguish between these alternatives, we first isolated laboratory strains ofChloroflexusOTU 10 from along the White Creek temperature gradient. These strains are identical for partial gene sequences encoding the 16S rRNA and malonyl coenzyme A (CoA) reductase. However, strains isolated from upstream and downstream samples could be distinguished based on sequence variation atpcs, which encodes the propionyl-CoA synthase of the 3-hydroxypropionate pathway of carbon fixation used by the genusChloroflexus. We next demonstrated that strains have diverged in temperature range for growth. Specifically, we obtained evidence for a positive correlation between thermal niche breadth and temperature optimum, with strains isolated from lower temperatures exhibiting greater thermal specialization than the most thermotolerant strain. The study has implications for our understanding of both the process of niche diversification of microorganisms and how diversity is organized in these hot spring communities.

scholarly journals Pseudomonas aeruginosa Clinical Isolates in Nepal Coproducing Metallo-β-Lactamases and 16S rRNA Methyltransferases

2017 ◽  
Vol 61 (9) ◽  
Author(s):  
Tatsuya Tada ◽  
Kayo Shimada ◽  
Kazuhito Satou ◽  
Takashi Hirano ◽  
Bharat M. Pokhrel ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
16S Rrna ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Content Type ◽  
First Report ◽  
Genes Encoding

ABSTRACT A total of 11 multidrug-resistant Pseudomonas aeruginosa clinical isolates were obtained in Nepal. Four of these isolates harbored genes encoding one or more carbapenemases (DIM-1, NDM-1, and/or VIM-2), and five harbored genes encoding a 16S rRNA methyltransferase (RmtB4 or RmtF2). A novel RmtF variant, RmtF2, had a substitution (K65E) compared with the same gene in RmtF. To our knowledge, this is the first report describing carbapenemase- and 16S rRNA methyltransferase-coproducing P. aeruginosa clinical isolates in Nepal.

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 ComparativeIn VitroActivities of SMT19969, a New Antimicrobial Agent, against 162 Strains from 35 Less Frequently Recovered Intestinal Clostridium Species: Implications for Clostridium difficile Recurrence

2013 ◽  
Vol 58 (2) ◽  
pp. 1187-1191 ◽  
Author(s):  
Ellie J. C. Goldstein ◽  
Diane M. Citron ◽  
Kerin L. Tyrrell
Keyword(s):  
Clostridium Difficile ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Antimicrobial Agent ◽  
Clostridium Species ◽  
Content Type ◽  
Comparative Activity

ABSTRACTWe determined the comparative activity of SMT19969 (SMT) against 162 strains representing 35 well-characterizedClostridiumspecies in clusters I to XIX and 13Clostridiumspecies that had no 16S rRNA match. SMT MICs ranged from 0.06 to >512 μg/ml and were not species related. SMT might have less impact on normal gut microbiota than otherClostridium difficileinfection (CDI) antimicrobials.

scholarly journals Effects of Industrial and Ruminant Trans-fatty Acids-Enriched Diet on Fecal Microbiome and Short Chain Fatty Acid Metabolites of C57BL/6 Mice

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 1171-1171
Author(s):  
Farzad Mohammadi ◽  
Emma Tolsdorf ◽  
Karine Greffard ◽  
Élodie Chotard ◽  
Jean-François Bilodeau ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Butyric Acid ◽  
Relative Abundance ◽  
Trans Fatty Acids ◽  
Valeric Acid ◽  
Short Chain ◽  
16S Rrna Analysis ◽  
Fecal Microbiome

Abstract Objectives We hypothesized that the intake of industrially originated trans-fatty acids (elaidic acid (EA trans 18: 1n-9)) and ruminant trans fatty acids (trans-palmitoleic acid (TPA t16:1 n-7)) will differentially modify gut microbiota and short-chain fatty acids (SCFA) profiles. The objective is to compare the long- and short-term effects of EA and TPA on the fecal microbiome and SCFAs profiles in mice. Methods Forty C57BL/6 mice were divided to 4 groups. Each group was given one of the following 4 formulations in the drinking water: lecithin nanovesicles, nanovesicles containing either lecithin with EA or TPA (86:14 (w/w)) or water alone (control) for 28 days with a normal fat diet. Fecal samples were collected at days 0, 7 and 28. Gut microbiota profiles were determined by 16S rRNA gene sequencing. SCFAs were measured by headspace gas chromatography coupled to a single quadrupole mass spectrometer. Baseline data (relative abundance of bacteria or levels of SCFAs) was pooled and then compared with data from day 7 or day 28 for each formulation. Results After 7 days of lecithin, 16S rRNA analysis revealed an increase in the relative abundance of Lactobacillus. After 28 days of lecithin, an increase in the relative abundance of Lactobacillus, Erysipelotrichaceae, and Enterobacteriaceae together with a decrease in Bacteroidaceae was observed. Further, a tendency to increase level of butyric acid (P = 0.053) was observed after 28 days of lecithin. After 7 days of EA, an increase in the relative abundance of Lactobacillus, whereas a decrease in the relative abundance of Parabacteroides, Bacteroides, Rumininococcaceae, Lachnospiraceae and Peptococcaceae was observed. After 7 days of TPA, results show a decreased level of isovaleric acid (P = 0.04) and valeric acid (P = 0.03). After 28 days of TPA, data demonstrates an increase in the level of butyric acid (P = 0.01) and propionic acid (P = 0.01). Water intake for 28 days decreased the level of valeric acid (P = 0.02). Conclusions Consumption of industrial and ruminant trans-fatty acids modify differentially bacterial taxa present in the gut microbiome and SCFA profiles. Funding Sources NSERC, CMDO.

scholarly journals Jian-Gan-Xiao-Zhi Decoction Alleviates Inflammatory Response in Nonalcoholic Fatty Liver Disease Model Rats through Modulating Gut Microbiota

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Jiabao Liao ◽  
Xuehua Xie ◽  
Jinmei Gao ◽  
Zhaiyi Zhang ◽  
Fei Qu ◽  
...  
Keyword(s):  
Liver Disease ◽  
16S Rrna ◽  
Inflammatory Response ◽  
Gut Microbiota ◽  
Fatty Liver ◽  
Fatty Liver Disease ◽  
Gut Permeability ◽  
16S Rrna Analysis ◽  
Nonalcoholic Fatty Liver ◽  
Tnf Α

Background. Jian-Gan-Xiao-Zhi decoction (JGXZ), composed of Salvia miltiorrhiza Bunge, Panax notoginseng, Curcuma zedoaria, and other 9 types of herbs, has demonstrated beneficial effects on nonalcoholic fatty liver disease (NAFLD). However, the mechanisms behind JGXZ’s impact on NAFLD remain unknown. Methods. In this study, a NAFLD rat model induced by a high-fat diet (HFD) received oral treatment of JGXZ (8 or 16 g crude herb/kg) for 12 weeks. The therapeutic effects of JGXZ on NAFLD model rats were investigated through blood lipid levels and pathological liver changes. 16S rRNA analysis was used to study the changes in gut microbiota after JGXZ treatment. The expressions of occludin and tight junction protein 1 (ZO-1) in the colon were investigated using immunostaining to study the effects of JGXZ on gut permeability. The anti-inflammatory effects of JGXZ were also studied through measuring the levels of IL-1β, IL-6, and TNF-α in the serum and liver. Results. JGXZ treatment could decrease body weight and ameliorate dyslipidemia in NAFLD model rats. H&E and Oil Red O staining indicated that JGXZ reduced steatosis and infiltration of inflammatory cells in the liver. 16S rRNA analysis showed that JGXZ impacted the diversity of gut microbiota, decreasing the Firmicutes–to-Bacteroidetes ratio, and increasing the relative abundance of probiotics, such as Alloprevotella, Lactobacillus, and Turicibacter. Gut permeability evaluation found that the expressions of ZO-1 and occludin in the colon were increased after JGXZ treatment. Moreover, JGXZ treatment could decrease the levels of IL-1β, IL-6, and TNF-α in the serum and liver. Conclusions. Our study illustrated that JGXZ could ameliorate NAFLD through modulating gut microbiota, decreasing gut permeability, and alleviating inflammatory response.

scholarly journals Fermented Milk Containing Lactobacillus casei Strain Shirota Preserves the Diversity of the Gut Microbiota and Relieves Abdominal Dysfunction in Healthy Medical Students Exposed to Academic Stress

2016 ◽  
Vol 82 (12) ◽  
pp. 3649-3658 ◽  
Author(s):  
Akito Kato-Kataoka ◽  
Kensei Nishida ◽  
Mai Takada ◽  
Mitsuhisa Kawai ◽  
Hiroko Kikuchi-Hayakawa ◽  
...  
Keyword(s):  
Placebo Group ◽  
Medical Students ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Lactobacillus Casei ◽  
Fermented Milk ◽  
Rrna Gene ◽  
Daily Consumption ◽  
Content Type ◽  
Abdominal Symptoms

ABSTRACTStress-induced abdominal dysfunction is an attractive target for probiotics. To investigate the effects of the probioticLactobacillus caseistrain Shirota on abdominal dysfunction, a double-blind, placebo-controlled trial was conducted with healthy medical students undertaking an authorized nationwide examination for academic advancement. For 8 weeks, until the day before the examination, 23 and 24 subjects consumed anL. caseistrain Shirota-fermented milk and a placebo milk daily, respectively. In addition to assessments of abdominal symptoms, psychophysical state, and salivary stress markers, gene expression changes in peripheral blood leukocytes and composition of the gut microbiota were analyzed using DNA microarray analysis and 16S rRNA gene amplicon sequence analysis, respectively, before and after the intervention. Stress-induced increases in a visual analog scale measuring feelings of stress, the total score of abdominal dysfunction, and the number of genes with changes in expression of more than 2-fold in leukocytes were significantly suppressed in theL. caseistrain Shirota group compared with those in the placebo group. A significant increase in salivary cortisol levels before the examination was observed only in the placebo group. The administration ofL. caseistrain Shirota, but not placebo, significantly reduced gastrointestinal symptoms. Moreover, 16S rRNA gene amplicon sequencing demonstrated that theL. caseistrain Shirota group had significantly higher numbers of species, a marker of the alpha-diversity index, in their gut microbiota and a significantly lower percentage ofBacteroidaceaethan the placebo group. Our findings indicate that the daily consumption of probiotics, such asL. caseistrain Shirota, preserves the diversity of the gut microbiota and may relieve stress-associated responses of abdominal dysfunction in healthy subjects exposed to stressful situations.IMPORTANCEA novel clinical trial was conducted with healthy medical students under examination stress conditions. It was demonstrated that the daily consumption of lactic acid bacteria provided health benefits to prevent the onset of stress-associated abdominal symptoms and a good change of gut microbiota in healthy medical students.

scholarly journals Kang-Xian Pills Inhibit Inflammatory Response and Decrease Gut Permeability to Treat Carbon Tetrachloride-Induced Chronic Hepatic Injury through Modulating Gut Microbiota

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Li Wang ◽  
Huantian Cui ◽  
Yuting Li ◽  
Min Cao ◽  
Shanshan Man ◽  
...  
Keyword(s):  
Carbon Tetrachloride ◽  
16S Rrna ◽  
Inflammatory Response ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Hepatic Injury ◽  
Gut Permeability ◽  
16S Rrna Analysis ◽  
Chronic Hepatic Injury ◽  
Anti Inflammatory

Kang-Xian (KX) pills have been clinically used for the treatment of chronic hepatic injury (CHI). However, the mechanisms of KX on CHI remain unknown. The aim of this study mainly focused on the anti-inflammatory effects of KX in a CHI mouse model based on modulating gut microbiota and gut permeability. We first established a CHI model using carbon tetrachloride (CCl4) and treated it with KX. The anti-inflammatory effects of KX on CHI model mice and the changes in gut permeability after KX treatment were also investigated. 16S rRNA analysis was used to study the changes of gut microbiota composition after KX treatment. In addition, gut microbiota was depleted using a combination of antibiotics in order to further confirm that KX could inhibit the inflammatory response and decrease gut permeability to treat CHI by modulating the gut microbiota. Results showed that KX treatment significantly improved liver function in CHI model mice. KX could also increase the levels of tight junction proteins in the colon and decrease the expression of proinflammatory cytokines in the liver. 16S rRNA analysis indicated that KX treatment affected the alpha and beta diversities in CHI model mice. Further analysis of 16S rRNA sequencing indicated that KX treatment increased the ratio of Firmicutes to Bacteroidetes at the phylum level. At the genus level, KX treatment increased the relative abundance of Lactobacillus, Bacteroides, and Akkermansia and decreased the relative abundance of Ralstonia, Alloprevotella, and Lachnoclostridium. However, KX could not alleviate CHI after depleting the gut microbiota. The effects of KX on gut permeability and inflammatory response in the liver were also decreased following the depletion of gut microbiota. In conclusion, our current study demonstrated that gut microbiota was significantly affected during CHI progression. KX could inhibit the inflammatory response and decrease the gut permeability in CHI model mice through modulating the gut microbiota.

scholarly journals Jian-Gan-Xiao-Zhi Decoction Ameliorates Nonalcoholic Fatty Liver Disease Through Modulating Gut Microbiota, Decreasing Gut Permeability, and Alleviating Liver Inflammation

2020 ◽  
Author(s):  
Jiabao Liao ◽  
Xuehua Xie ◽  
Jinmei Gao ◽  
Zhaiyi Zhang ◽  
Fei Qv ◽  
...  
Keyword(s):  
Liver Disease ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Fatty Liver ◽  
Fatty Liver Disease ◽  
Liver Inflammation ◽  
Gut Permeability ◽  
16S Rrna Analysis ◽  
Nonalcoholic Fatty Liver ◽  
Tnf Α

Abstract BackgroundJian-Gan-Xiao-Zhi decoction (JGXZ), composed of Salvia miltiorrhiza Bunge, Panax notoginseng, Curcuma zedoaria, and other 9 types of herbs, has demonstrated beneficial effects on nonalcoholic fatty liver disease (NAFLD). However, the mechanisms behind JGXZ’s impact on NAFLD remain unknown. MethodsIn this study, a NAFLD rat model induced by a high-fat diet (HFD) received oral treatment of JGXZ (8 or 16 g crude herb/kg) for 8 weeks. The therapeutic effects of JGXZ on NAFLD model rats were investigated through blood lipid levels and pathological liver changes. 16s rRNA analysis was used to study the changes in gut microbiota after JGXZ treatment. The expressions of occludin and tight junction protein 1 (ZO-1) in colon were investigated using immunostaining to study the effects of JGXZ on gut permeability. The anti-inflammatory effects of JGXZ were also studied through measuring the levels of IL-1β, IL-6 and TNF-α in serum and liver.ResultsJGXZ treatment could decrease body weight and ameliorate dyslipidemia in NAFLD model rats. H&E and Oil Red O staining indicated that JGXZ reduced steatosis and infiltration of inflammatory cells into the liver. 16s rRNA analysis exhibited that JGXZ impacted the diversity of gut microbiota, decreasing the Firmicutes to Bacteroidetes ratio and increasing the relative abundance of probiotics, such as Alloprevotella, Lactobacillus, and Turicibacter. Gut permeability evaluation found that the expressions of ZO-1 and occludin in the colon were increased after JGXZ treatment, and inflammation analysis showed decreased levels of IL-1β, IL-6, and TNF-α in the serum and liver after treatment. ConclusionsOur study illustrates that JGXZ ameliorates NAFLD through modulating gut microbiota, decreasing gut permeability, and alleviating liver inflammation.

Sign in / Sign up

Export Citation Format

Share Document