scholarly journals A longitudinal study of the faecal microbiome and metabolome of periparturient mares

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6687 ◽  
Author(s):  
Shebl E. Salem ◽  
Rachael Hough ◽  
Chris Probert ◽  
Thomas W. Maddox ◽  
Philipp Antczak ◽  
...  

Background Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares. Methods Faecal samples were collected weekly from five pregnant mares from 3 weeks pre-foaling to 7 weeks post-foaling. The microbiome data was generated by PCR amplification and sequencing of the V1–V2 regions of the bacterial 16S rRNA genes, while the VOC profile was characterised using headspace solid phase microextraction gas chromatography mass spectrometry. Results The mare faecal microbiota was relatively stable over the periparturient period and most variation was associated with individual mares. A small number of operational taxonomic units were found to be significantly differentially abundant between samples collected before and after foaling. A total of 98 VOCs were identified. The total number of VOCs did not vary significantly between individual mares, weeks of sample collection and feeds available to the mares. Three VOCs (decane, 2-pentylfuran, and oct-2-ene) showed significant increase overtime on linear mixed effects modelling analysis. These results suggest that the mare faecal microbiota is structurally and functionally stable during the periparturient period. The findings also suggest that if changes in the gut microbiota are related to development of colic postpartum, altered risk may be due to inherent differences between individual mares. VOCs offer a cost-effective means of looking at the functional changes in the microbiome and warrant further investigation in mares at risk of colic.

2019 ◽  
Author(s):  
Shebl Ebrahim Salem ◽  
Thomas W Maddox ◽  
Philipp Antczak ◽  
Julian M Ketley ◽  
Nicola J Williams ◽  
...  

Abstract Abstract Background Horses that undergo surgery for treatment of primary large colon disease have been reported to be at increased risk of developing recurrent colic episodes postoperatively. The reasons for this are currently unknown. The aim of the current study was to characterise the faecal microbiota of horses with colic signs associated with primary large colon lesions treated surgically and to compare the composition of their faecal microbiota to that of a control group of horses undergoing emergency orthopaedic treatment. Faecal samples were collected from horses in both groups on admission to hospital, during hospitalisation and following discharge from hospital for a total duration of 12 weeks. Additionally, colonic content samples were collected from surgical colic patients if pelvic flexure enterotomy was performed during laparotomy. A total of 12 samples were collected per horse. DNA was extracted from samples using a commercial kit. Amplicon mixtures were created by PCR amplification of the V1 – V2 regions of the bacterial 16S rRNA genes and submitted for sequencing using the Ion Torrent PGM next-generation sequencing system. Multivariate data analysis was used to characterise the faecal microbiota and to investigate differences between groups. Results Reduced species richness was evident in the colonic samples of the colic group compared to concurrent sampling of the faeces. Alpha and beta diversity differed significantly between the two sets of samples with 304 significantly differentially abundant OTUs identified. Only 46 OTUs varied significantly between the colic and control group. There were no significant differences in alpha and beta diversity of faecal microbiota between colic and control horses at admission. Conclusions The results of the current study suggest that faecal samples collected at hospital admission in colic cases may not accurately represent changes in upper gut microbiota in horses with colic due to large colon disease.


2003 ◽  
Vol 69 (3) ◽  
pp. 1614-1622 ◽  
Author(s):  
P. Padmanabhan ◽  
S. Padmanabhan ◽  
C. DeRito ◽  
A. Gray ◽  
D. Gannon ◽  
...  

ABSTRACT Our goal was to develop a field soil biodegradation assay using 13C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived 13C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of 13C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for 13CO2 respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of 13CO2 emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF6, that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired 13CO2. Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of 13CO2 released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of 13C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with 13C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of Arthrobacter, Pseudomonas, Acinetobacter, Massilia, Flavobacterium, and Pedobacter spp. for glucose; Pseudomonas, Pantoea, Acinetobacter, Enterobacter, Stenotrophomonas, and Alcaligenes spp. for phenol; Pseudomonas, Acinetobacter, and Variovorax spp. for naphthalene; and Acinetobacter, Enterobacter, Stenotrophomonas, and Pantoea spp. for caffeine.


2011 ◽  
Vol 108 (6) ◽  
pp. 953-957 ◽  
Author(s):  
Jayakanthan Kabeerdoss ◽  
R. Shobana Devi ◽  
R. Regina Mary ◽  
Balakrishnan S. Ramakrishna

The effect of vegetarian diets on faecal microbiota has been explored largely through culture-based techniques. The present study compared the faecal microbiota of vegetarian and omnivorous young women in southern India. Faecal samples were obtained from thirty-two lacto-vegetarian and twenty-four omnivorous young adult women from a similar social and economic background. Macronutrient intake and anthropometric data were collected. Faecal microbiota of interest was quantified by real-time PCR with SYBR Green using primers targeting 16S rRNA genes of groups, including: Clostridium coccoides group (Clostridium cluster XIVa), Roseburia spp.–Eubacterium rectale, Bacteroides–Prevotella group, Bifidobacterium genus, Lactobacillus group, Clostridium leptum group (Clostridium cluster IV), Faecalibacterium prausnitzii, Ruminococcus productus–C. coccoides, Butyrivibrio, Enterococcus species and Enterobacteriaceae. The groups were matched for age, socio-economic score and anthropometric indices. Intake of energy, complex carbohydrates and Ca were significantly higher in the omnivorous group. The faecal microbiota of the omnivorous group was enriched with Clostridium cluster XIVa bacteria, specifically Roseburia–E. rectale. The relative proportions of other microbial communities were similar in both groups. The butyryl-CoA CoA-transferase gene, associated with microbial butyrate production, was present in greater amounts in the faeces of omnivores, and the levels were highly correlated with Clostridium cluster XIVa and Roseburia–E. rectale abundance and to a lesser extent with Clostridium leptum and F. prausnitzii abundance and with crude fibre intake. Omnivores had an increased relative abundance of Clostridium cluster XIVa bacteria and butyryl-CoA CoA-transferase gene compared with vegetarians, but we were unable to identify the components of the diet responsible for this difference.


2004 ◽  
Vol 50 (5) ◽  
pp. 15-22 ◽  
Author(s):  
S.J. Khan ◽  
T. Wintgens ◽  
P. Sherman ◽  
J. Zaricky ◽  
A.I. Schäfer

An advanced water recycling demonstration plant was employed to investigate the effectiveness of a number of treatment technologies in the removal of some residuals of commonly prescribed pharmaceuticals as well as natural and synthetic hormones found in sewage. Analysis of targeted compounds was carried out by solid-phase extraction (SPE) and gas chromatography-mass spectrometry (GC-MS). Initial tests were undertaken to determine the background concentrations of the analytes during various stages of treatment. Subsequent tests, undertaken by spiking with standard solutions of the target compounds provided further information on the removal efficiencies of some selected treatment modules. The results of the study indicate that while ozonation, microfiltration and nanofiltration were partially effective, treatment by reverse osmosis was the most universally successful in the removal of the target residuals. While significantly more data is required for a full evaluation, this initial investigation suggests that reverse osmosis may be an effective means of removing a wider range of pharmaceutically active residuals and hormones from treated sewage.


mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Alyxandria M. Schubert ◽  
Mary A. M. Rogers ◽  
Cathrin Ring ◽  
Jill Mogle ◽  
Joseph P. Petrosino ◽  
...  

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.


Molecules ◽  
2020 ◽  
Vol 25 (1) ◽  
pp. 179 ◽  
Author(s):  
Yasser S. Mostafa ◽  
Sulaiman A. Alrumman ◽  
Kholod A. Otaif ◽  
Saad A. Alamri ◽  
Mohamed S. Mostafa ◽  
...  

The synthesis of bioplastic from marine microbes has a great attendance in the realm of biotechnological applications for sustainable eco-management. This study aims to isolate novel strains of poly-β-hydroxybutyrate (PHB)-producing bacteria from the mangrove rhizosphere, Red Sea, Saudi Arabia, and to characterize the extracted polymer. The efficient marine bacterial isolates were identified by the phylogenetic analysis of the 16S rRNA genes as Tamlana crocina, Bacillus aquimaris, Erythrobacter aquimaris, and Halomonas halophila. The optimization of PHB accumulation by E. aquimaris was achieved at 120 h, pH 8.0, 35 °C, and 2% NaCl, using glucose and peptone as the best carbon and nitrogen sources at a C:N ratio of 9.2:1. The characterization of the extracted biopolymer by Fourier-transform infrared spectroscopy (FTIR), Nuclear magnetic resonance (NMR), and Gas chromatography-mass spectrometry (GC-MS) proves the presence of hydroxyl, methyl, methylene, methine, and ester carbonyl groups, as well as derivative products of butanoic acid, that confirmed the structure of the polymer as PHB. This is the first report on E. aquimaris as a PHB producer, which promoted the hypothesis that marine rhizospheric bacteria were a new area of research for the production of biopolymers of commercial value.


2020 ◽  
Vol 5 (3) ◽  
pp. 1-11
Author(s):  
Miambi E

Termites are examples of natural biomass utilization systems that have evolved to overcome the recalcitrance of lignin to degradation. To investigate the application of this to the conversion of technical lignins produced by biorefineries, a higher wood-feeding termite species, Nasutitermes ephratae, was fed with a commercial grass soda lignin (Protobind 1000, PB1000). We investigated the fate of PB1000 in termite guts and the changes in gut microbiota that occurred using Pyrolysis - Gas Chromatography / Mass Spectrometry (Py-GC/MS) and high-throughput sequencing of the 16S rRNA genes. The worker caste termites fed with PB1000 had only half the survival rate of the controls and increased the PB1000 syringyl/guaiacyl ratio from 1.74 to 2.26. The changes in the syringyl/guaiacyl ratio were consistent with the degradation of the free phenolic monomers in PB1000 inside the termite gut, and they were associated with the increase in the relative abundance of Firmicutes and Bacteroidetes. This work showed the ability of the digestive tract of a wood-feeding higher termite species, N. ephratae, to metabolize the free-volatile phenolic monomers in PB1000. Overall, our results identified bacterial candidates for the development of a bacterial inoculum in pretreatment processes for the utilization of technical lignin in biorefineries.


Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 6027
Author(s):  
Heting Qi ◽  
Shenghua Ding ◽  
Zhaoping Pan ◽  
Xiang Li ◽  
Fuhua Fu

Citrus tea is an emerging tea drink produced from tea and the pericarp of citrus, which consumers have increasingly favored due to its potential health effects and unique flavor. This study aimed to simultaneously combine the characteristic volatile fingerprints with the odor activity values (OAVs) of different citrus teas for the first time by headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS) and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results showed that the establishment of a citrus tea flavor fingerprint based on HS-GC-IMS data can provide an effective means for the rapid identification and traceability of different citrus varieties. Moreover, 68 volatile compounds (OAV > 1) were identified by HS-SPME-GC-MS, which reflected the contribution of aroma compounds to the characteristic flavor of samples. Amongst them, the contribution of linalool with sweet flower fragrance was the highest. Odorants such as decanal, β-lonone, β-ionone, β-myrcene and D-limonene also contributed significantly to all samples. According to principal component analysis, the samples from different citrus teas were significantly separated. Visualization analysis based on Pearson correlation coefficients suggested that the correlation between key compounds was clarified. A comprehensive evaluation of the aroma of citrus tea will guide citrus tea flavor quality control and mass production.


2019 ◽  
Author(s):  
Hila Korach-Rechtman ◽  
Maysaa Hreish ◽  
Carmit Fried ◽  
Shiran Gerassy-Vainberg ◽  
Zaher S Azzam ◽  
...  

AbstractInfection with Carbapenem-Resistant Enterobacteriaceae (CRE) became an important challenge in health-care settings and a growing concern worldwide. Since infection is preceded by colonization, an understanding of the latter may reduce CRE-infections. We aimed to characterize the gut microbiota after colonization by CRE, assuming that an imbalanced gastrointestinal tract (GIT)-associated microbiota precedes CRE-colonization.We evaluated the GIT-microbiota using 16S rRNA genes sequencing extracted of fecal samples, collected from hospitalized CRE-carriers, and two control groups of hospitalized non-carriers and healthy adults. The microbiota diversity and composition in CRE-colonized patients differed from that of the control groups participants. These CRE-carriers displayed lower phylogenetic diversity and dysbiotic microbiota, enriched with members of the Enterobacteriaceae family. Concurrent with the bloom in Enterobacteriaceae, a depletion of anaerobic commensals was observed. Additionally, changes in several predicted metabolic pathways were observed for the CRE-carriers. Concomitant, we found higher prevalence of bacteremia in the CRE-carriers.Several clinical factors that might induce change in the microbiota were examined and found as insignificant between the groups.CRE-colonized patients have dysbiotic gut microbiota in terms of diversity and community membership, associated with increased risk for systemic infection. Our study results provides justification for attempts to restore the dysbiotic microbiota with probiotics or fecal transplantation.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 358-358 ◽  
Author(s):  
Christoph K. Stein-Thoeringer ◽  
Jonathan U. Peled ◽  
Antonio LC Gomes ◽  
Amina Lazrak ◽  
Melissa D Docampo ◽  
...  

Abstract Introduction: Increasing evidence suggests that the intestinal microbiota is involved in the development of acute graft-vs.-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT). We previously reported in single center studies that Enterococcus a) is associated with GVHD (Holler et al., BBMT 2014) and b) can dominate the post-transplant gut microbiota in up to 50% of allo-HCT patients resulting in a 9-fold increased risk of bacteremia (Taur et al, CID 2012). To further investigate the hypothesis that Enterococcus can trigger the development of GVHD, we studied both allo-HCT patients and pre-clinical mouse transplant models. Methods and Results: Stool samples from 1240 allo-HCT patients at 4 different transplant centers in the U.S., Germany and Japan were collected approximately weekly during inpatient hospitalization. The V4-V5 region of the bacterial 16S rRNA genes from 6718 samples was sequenced at one central site on the Illumina platform. We observed Enterococcus mono-domination (relative abundance > 30%) in post-transplant samples ranging from 20 to 60% of patients at different centers (Fig. A, left). This mono-domination was primarily attributable to E. faecium, and was associated with a significantly increased risk for grade 2-4 acute GVHD (Fig. A, right). In three different mouse models we found a transient bloom of E. faecalis around 7 days after transplant in allo-HCT recipients with GVHD (Fig. B; C57BL/6 -> 129SV model). This bloom did not occur in allo-HCT recipients of a T cell depleted allograft without GVHD. To further investigate this Enterococcus bloom, we treated mice with an experimental E. faecalis-strain on days 4 to 6 after transplant and found significantly increased lethal GVHD. Colonizing germ-free mice with a minimal gut flora also lead to increased lethal GVHD when enterococci were added to the gnotobiotic flora (Fig. C). The allo-HCT recipients with Enterococcus-containing flora had also increased serum IFNg levels. Short chain fatty acids (SCFA) can be protective against GVHD and gut inflammation through maintenance of epithelial homeostasis and increases in anti-inflammatory regulatory T cells in the gut. In BMT mouse models, we found that Enterococcus-dominated allo-HCT recipients with GVHD have significantly less cecal butyrate, a major SCFA. Similarly, Enterococcus domination after allo-HCT also leads to a decrease in fecal SCFAs in patients (Fig. D). Next, we hypothesized that intestinal IgA might have a protective role against this pathogen in mice. 16S sequencing of flow sorted IgA-coated vs. non-coated bacteria from fecal samples of allo-HCT patients and transplanted mice revealed no specific IgA-coating pattern of enterococci both before or after transplant rather excluding the hypothesis that IgA might have a protective role against Enterococci. E. faecalis and E. faecium use the disaccharide lactose as a major carbohydrate source for growth and expansion as observed by analyses of the Enterococcus genome and in vitro growth experiments. In mice, we observed that a lactose-free diet significantly decreases the Enterococcus bloom after transplant in allo-T cell recipients and in first survival experiments attenuates lethal GVHD (Fig. E). Conclusion: Our studies in mouse and man demonstrate that the abundance of Enterococcus in the intestinal flora plays a role in the development of GVHD and the prevention of Enterococcus growth with a lactose-free diet can ameliorate GVHD. Disclosures Peled: Seres Therapeutics: Research Funding.


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