Publications by authors named "Eric Pinloche"

18 Publications

  • Page 1 of 1

Bacillus Subtilis 29784 as a Feed Additive for Broilers Shifts the Intestinal Microbial Composition and Supports the Production of Hypoxanthine and Nicotinic Acid.

Animals (Basel) 2021 May 8;11(5). Epub 2021 May 8.

Livestock Gut Health Team, Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.

The probiotic strain 29784 (Bs29784) has been shown to improve performance in broilers. In this study, we used a metabolomic and 16S rRNA gene sequencing approach to evaluate effects of Bs29874 in the broiler intestine. Nicotinic acid and hypoxanthine were key metabolites that were produced by the strain in vitro and were also found in vivo to be increased in small intestinal content of broilers fed Bs29784 as dietary additive. Both metabolites have well-described anti-inflammatory effects in the intestine. Furthermore, Bs29784 supplementation to the feed significantly altered the ileal microbiome of 13-day-old broilers, thereby increasing the abundance of genus , while decreasing genera and OTUs belonging to the and families. Moreover, Bs29784 did not change the cecal microbial community structure, but specifically enriched members of the family , as well as the butyrate-producing families and The abundance of various OTUs and genera belonging to these families was significantly associated with nicotinic acid levels in the cecum, suggesting a possible cross-feeding between strain 29784 and these beneficial microbes. Taken together, the data indicate that Bs29784 exerts its described probiotic effects through a combined action of its metabolites on both the host and its microbiome.
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http://dx.doi.org/10.3390/ani11051335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8150382PMC
May 2021

The Multifunctional Sactipeptide Ruminococcin C1 Displays Potent Antibacterial Activity In Vivo as Well as Other Beneficial Properties for Human Health.

Int J Mol Sci 2021 Mar 23;22(6). Epub 2021 Mar 23.

CNRS, Aix-Marseille University, Centrale Marseille, iSm2, 13013 Marseille, France.

The world is on the verge of a major antibiotic crisis as the emergence of resistant bacteria is increasing, and very few novel molecules have been discovered since the 1960s. In this context, scientists have been exploring alternatives to conventional antibiotics, such as ribosomally synthesized and post-translationally modified peptides (RiPPs). Interestingly, the highly potent in vitro antibacterial activity and safety of ruminococcin C1, a recently discovered RiPP belonging to the sactipeptide subclass, has been demonstrated. The present results show that ruminococcin C1 is efficient at curing infection and at protecting challenged mice from with a lower dose than the conventional antibiotic vancomycin. Moreover, antimicrobial peptide (AMP) is also effective against this pathogen in the complex microbial community of the gut environment, with a selective impact on a few bacterial genera, while maintaining a global homeostasis of the microbiome. In addition, ruminococcin C1 exhibits other biological activities that could be beneficial for human health, as well as other fields of applications. Overall, this study, by using an in vivo infection approach, confirms the antimicrobial clinical potential and highlights the multiple functional properties of ruminococcin C1, thus extending its therapeutic interest.
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http://dx.doi.org/10.3390/ijms22063253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005207PMC
March 2021

2-Hydroxy-(4-methylseleno)butanoic Acid Is Used by Intestinal Caco-2 Cells as a Source of Selenium and Protects against Oxidative Stress.

J Nutr 2019 12;149(12):2191-2198

Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain.

Background: Selenium (Se) participates in different functions in humans and other animals through its incorporation into selenoproteins as selenocysteine. Inadequate dietary Se is considered a risk factor for several chronic diseases associated with oxidative stress.

Objective: The role of 2-hydroxy-(4-methylseleno)butanoic acid (HMSeBA), an organic form of Se used in animal nutrition, in supporting selenoprotein synthesis and protecting against oxidative stress was investigated in an in vitro model of intestinal Caco-2 cells.

Methods: Glutathione peroxidase (GPX) and thioredoxin reductase (TXNRD) activities, selenoprotein P1 protein (SELENOP) and gene (SELENOP) expression, and GPX1 and GPX2 gene expression were studied in Se-deprived (FBS removal) and further HMSeBA-supplemented (0.1-625 μM, 72 h) cultures. The effect of HMSeBA supplementation (12.5 and 625 μM, 24 h) on oxidative stress induced by H2O2 (1 mM) was evaluated by the production of reactive oxygen species (ROS), 4-hydroxy-2-nonenal (4-HNE) adducts, and protein carbonyl residues compared with a sodium selenite control (SS, 5 μM).

Results: Se deprivation induced a reduction (P < 0.05) in GPX activity (62%), GPX1 expression, and both SELENOP (33%) and SELENOP expression. In contrast, an increase (P < 0.05) in GPX2 expression and no effect in TXNRD activity (P = 0.09) were observed. HMSeBA supplementation increased (P < 0.05) GPX activity (12.5-625 μM, 1.68-1.82-fold) and SELENOP protein expression (250 and 625 μM, 1.87- and 2.04-fold). Moreover, HMSeBA supplementation increased (P < 0.05) GPX1 (12.5 and 625 μM), GPX2 (625 μM), and SELENOP (12.5 and 625 μM) expression. HMSeBA (625 μM) was capable of decreasing (P < 0.05) ROS (32%), 4-HNE adduct (49%), and protein carbonyl residue (75%) production after H2O2 treatment.

Conclusion: Caco-2 cells can use HMSeBA as an Se source for selenoprotein synthesis, resulting in protection against oxidative stress.
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http://dx.doi.org/10.1093/jn/nxz190DOI Listing
December 2019

Using next-generation sequencing to determine diversity of horse intestinal worms: identifying the equine 'nemabiome'.

J Equine Sci 2019 Mar 3;30(1):1-5. Epub 2019 Apr 3.

Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, SY23 3DA Wales, U.K.

Next-generation sequencing of DNA from nematode eggs has been utilised to give the first account of the equine 'nemabiome'. In all equine faecal samples investigated, multiple species of Strongylidae were detected, ranging from 7.5 (SEM 0.79) with 99+% identity to sequences in the NCBI database to 13.3 (SEM 0.80) with 90+% identity. This range is typical of the number of species described previously in morphological studies using large quantities of digesta per animal. However, the current method is non-invasive; relies on DNA analysis, avoiding the need for specialist microscopy identification; and can be carried out with small samples, providing significant advantages over current methods.
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http://dx.doi.org/10.1294/jes.30.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445754PMC
March 2019

Analysis of the Rumen Microbiome and Metabolome to Study the Effect of an Antimethanogenic Treatment Applied in Early Life of Kid Goats.

Front Microbiol 2018 9;9:2227. Epub 2018 Oct 9.

Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.

This work aimed to gain insight into the transition from milk to solid feeding at weaning combining genomics and metabolomics on rumen contents from goat kids treated with a methanogenic inhibitor (bromochloromethane, BCM). Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with BCM after giving birth and over 2 months. One kid per doe in both groups was treated with BCM (k+) for 3 months while the other was untreated (k-). Rumen samples were collected from kids at weaning (W) and 1 (W + 1) and 4 (W + 4) months after and from does at weaning and subjected to 16S pyrosequencing and metabolomics analyses combining GC/LC-MS. Results from pyrosequencing showed a clear effect of age of kids, with more diverse bacterial community as solid feed becomes more important after weaning. A number of specific OTUs were significantly different as a result of BCM treatment of the kid at W while at W + 1 and W + 4 less OTUs were significantly changed. At W + 1, was increased and decreased in BCM treated kids. At W + 4 only the effect of treating mothers resulted in significant changes in the abundance of some OTUs: and . The analysis of the OTUs shared by different treatments revealed that kids at weaning had the largest number of unique OTUs compared with kids at W + 1 (137), W + 4 (238), and does (D) (23). D + k+ kids consistently shared more OTUs with mothers than the other three groups at the three sampling times. The metalobomic study identified 473 different metabolites. In does, lipid super pathway included the highest number of metabolites that were modified by BCM, while in kids all super-pathways were evenly affected. The metabolomic profile of samples from kids at W was different in composition as compared to W + 1 and W + 4, which may be directly ascribed to the process of rumen maturation and changes in the solid diet. This study shows the complexity of the bacterial community and metabolome in the rumen before weaning, which clearly differ from that after weaning and highlight the importance of the dam in transmitting the primary bacterial community after birth.
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http://dx.doi.org/10.3389/fmicb.2018.02227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6189281PMC
October 2018

Characterization and anti-salmonella activities of lactic acid bacteria isolated from cattle faeces.

BMC Microbiol 2018 08 30;18(1):96. Epub 2018 Aug 30.

Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.

Background: Non typhoidal salmonellosis is one of the neglected zoonoses in most African countries. The use of sub-therapeutic doses of antibiotics as animal growth promoter enhances the emergence and dissemination of antimicrobial resistance in bacteria with food animal reservoirs and may also results in antibiotics residue in animal products. One promising alternative to antibiotics in animal feed is Lactic Acid Bacteria (LAB) as probiotics. This study was carried out to determine the anti-salmonella activities and suitability of LAB isolated from cattle faeces in Nigeria as potential probiotics in cattle feed.

Method: The test Salmonella enterica spp strains and LAB were isolated from cattle faeces and identified by MALDI-TOF MS and partial sequencing of 16S rRNA genes respectively. The anti-salmonella activities of the isolated LAB in co-culture, cell-free supernatant, inhibition of growth by viable LAB cells and quantification of organic acids were determined by standard techniques. The ability of the LAB strains to withstand gastric conditions, antibiotic susceptibility and their haemolytic ability on blood agar were also determined.

Results: A total of 88 LAB belonging to 15 species were isolated and identified from cattle faeces. The most abundant species were Streptococcus infantarius (26), Enterococcus hirae (12), Lactobacillus amylovorus (10), Lactobacillus mucosae (10) and Lactobacillus ingluviei (9). Most of the LAB strains showed good anti-salmonella activities against the test Salmonella enterica spp. with 2 Lactobacillus strains; Lactobacillus amylovorus C94 and Lactobacillus salivarius C86 exhibiting remarkable anti-salmonella activities with total inhibition of Salmonella spp after 18 hours of co-incubation. The selected strains were able to survive simultaneous growth at pH 3 and 7% bile concentration and are non hemolytic.

Conclusion: This study reports the vast diversity of culturable LAB in cattle faeces from Nigeria and their putative in-vitro antibacterial activity against Salmonella enterica spp isolated from cattle. Lactobacillus amylovorus C94 and Lactobacillus salivarius C86 demonstrated promising probiotic potentials in-vitro and will be further tested in-vivo in animal field trial.
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http://dx.doi.org/10.1186/s12866-018-1248-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118008PMC
August 2018

Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats.

PLoS One 2017 16;12(8):e0182235. Epub 2017 Aug 16.

Estación Experimental del Zaidín (CSIC), Granada, Spain.

The aim of this work was to evaluate the effect of feeding management during the first month of life (natural with the mother, NAT, or artificial with milk replacer, ART) on the rumen microbial colonization and the host innate immune response. Thirty pregnant goats carrying two fetuses were used. At birth one kid was taken immediately away from the doe and fed milk replacer (ART) while the other remained with the mother (NAT). Kids from groups received colostrum during first 2 days of life. Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 7, 14, 21 and 28 days of life. On the sampling day, after slaughtering, the rumen content was sampled and epithelial rumen tissue was collected. Pyrosequencing analyses of the bacterial community structure on samples collected at 3, 7, 14 and 28 days showed that both systems promoted significantly different colonization patterns (P = 0.001). Diversity indices increased with age and were higher in NAT feeding system. Lower mRNA abundance was detected in TLR2, TLR8 and TLR10 in days 3 and 5 compared to the other days (7, 14, 21 and 28). Only TLR5 showed a significantly different level of expression according to the feeding system, presenting higher mRNA abundances in ART kids. PGLYRP1 showed significantly higher abundance levels in days 3, 5 and 7, and then experienced a decline independently of the feeding system. These observations confirmed a highly diverse microbial colonisation from the first day of life in the undeveloped rumen, and show that the colonization pattern substantially differs between pre-ruminants reared under natural or artificial milk feeding systems. However, the rumen epithelial immune development does not differentially respond to distinct microbial colonization patterns.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182235PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558975PMC
October 2017

Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique.

FEMS Microbiol Ecol 2016 Jan 15;92(1). Epub 2015 Dec 15.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, Aberystwyth, UK.

This study investigates the effects of supplementing a control diet (CON) with chitosan (CHI) or ivy fruit saponins (IVY) as natural feed additives. Both additives had similar abilities to decrease rumen methanogenesis (-42% and -40%, respectively) using different mechanisms: due to its antimicrobial and nutritional properties CHI promoted a shift in the fermentation pattern towards propionate production which explained about two thirds of the decrease in methanogenesis. This shift was achieved by a simplification of the structure in the bacterial community and a substitution of fibrolytic (Firmicutes and Fibrobacteres) by amylolytic bacteria (Bacteroidetes and Proteobacteria) which led to greater amylase activity, lactate and microbial protein yield with no detrimental effect on feed digestibility. Contrarily, IVY had negligible nutritional properties promoting minor changes in the fermentation pattern and on the bacterial community. Instead, IVY modified the structure of the methanogen community and decreased its diversity. This specific antimicrobial effect of IVY against methanogens was considered its main antimethanogenic mechanism. IVY had however a negative impact on microbial protein synthesis. Therefore, CHI and IVY should be further investigated in vivo to determine the optimum doses which maintain low methanogenesis but prevent negative effects on the rumen fermentation and animal metabolism.
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http://dx.doi.org/10.1093/femsec/fiv160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831848PMC
January 2016

Pros and cons of ion-torrent next generation sequencing versus terminal restriction fragment length polymorphism T-RFLP for studying the rumen bacterial community.

PLoS One 2014 22;9(7):e101435. Epub 2014 Jul 22.

Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.

The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101435PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4106765PMC
March 2016

Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing.

PLoS One 2014 4;9(2):e87424. Epub 2014 Feb 4.

Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.

Faecal samples were collected from seventeen animals, each fed three different diets (high fibre, high fibre with a starch rich supplement and high fibre with an oil rich supplement). DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the faecal microbiome of the horse. The effect of age was also considered by comparing mature (8 horses aged 5-12) versus elderly horses (9 horses aged 19-28). A reduction in diversity was found in the elderly horse group. Significant differences between diets were found at an OTU level (52 OTUs at corrected Q<0.1). The majority of differences found were related to the Firmucutes phylum (37) with some changes in Bacteroidetes (6), Proteobacteria (3), Actinobacteria (2) and Spirochaetes (1). For the forage only diet,with no added starch or oil, we found 30/2934 OTUs (accounting for 15.9% of sequences) present in all horses. However the core (i.e. present in all horses) associated with the oil rich supplemented diet was somewhat smaller (25/3029 OTUs, 10.3% ) and the core associated with the starch rich supplemented diet was even smaller (15/2884 OTUs, 5.4% ). The core associated with samples across all three diets was extremely small (6/5689 OTUs accounting for only 2.3% of sequences) and dominated by the order Clostridiales, with the most abundant family being Lachnospiraceae. In conclusion, forage based diets plus starch or oil rich complementary feeds were associated with differences in the faecal bacterial community compared with the forage alone. Further, as observed in people, ageing is associated with a reduction in bacterial diversity. However there was no change in the bacterial community structure in these healthy animals associated with age.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087424PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913607PMC
December 2014

Identification of a core bacterial community within the large intestine of the horse.

PLoS One 2013 24;8(10):e77660. Epub 2013 Oct 24.

Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.

The horse has a rich and complex microbial community within its gastrointestinal tract that plays a central role in both health and disease. The horse receives much of its dietary energy through microbial hydrolysis and fermentation of fiber predominantly in the large intestine/hindgut. The presence of a possible core bacterial community in the equine large intestine was investigated in this study. Samples were taken from the terminal ileum and 7 regions of the large intestine from ten animals, DNA extracted and the V1-V2 regions of 16SrDNA 454-pyrosequenced. A specific group of OTUs clustered in all ileal samples and a distinct and different signature existed for the proximal regions of the large intestine and the distal regions. A core group of bacterial families were identified in all gut regions with clear differences shown between the ileum and the various large intestine regions. The core in the ileum accounted for 32% of all sequences and comprised of only seven OTUs of varying abundance; the core in the large intestine was much smaller (5-15% of all sequences) with a much larger number of OTUs present but in low abundance. The most abundant member of the core community in the ileum was Lactobacillaceae, in the proximal large intestine the Lachnospiraceae and in the distal large intestine the Prevotellaceae. In conclusion, the presence of a core bacterial community in the large intestine of the horse that is made up of many low abundance OTUs may explain in part the susceptibility of horses to digestive upset.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077660PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812009PMC
August 2014

Strong stability and host specific bacterial community in faeces of ponies.

PLoS One 2013 11;8(9):e75079. Epub 2013 Sep 11.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales.

The horse, as a hindgut fermenter, is reliant on its intestinal bacterial population for efficient diet utilisation. However, sudden disturbance of this population can result in severe colic or laminitis, both of which may require euthanasia. This study therefore aimed to determine the temporal stability of the bacterial population of faecal samples from six ponies maintained on a formulated high fibre diet. Bacterial 16S rRNA terminal restriction fragment length polymorphism (TRFLP) analyses of 10 faecal samples collected from 6 ponies at regular intervals over 72 hour trial periods identified a significant pony-specific profile (P<0.001) with strong stability. Within each pony, a significantly different population was found after 11 weeks on the same diet (P<0.001) and with greater intra-individual similarity. Total short chain fatty acid (SCFA) concentration increased in all ponies, but other changes (such as bacterial population diversity measures, individual major SCFA concentration) were significant and dependent on the individual. This study is the first to report the extent of stability of microbes resident in the intestinal tract as represented with such depth and frequency of faecal sampling. In doing so, this provides a baseline from which future trials can be planned and the extent to which results may be interpreted.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075079PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770578PMC
July 2014

Identification and characterization of three novel lipases belonging to families II and V from Anaerovibrio lipolyticus 5ST.

PLoS One 2013 12;8(8):e69076. Epub 2013 Aug 12.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK.

Following the isolation, cultivation and characterization of the rumen bacterium Anaerovibrio lipolyticus in the 1960s, it has been recognized as one of the major species involved in lipid hydrolysis in ruminant animals. However, there has been limited characterization of the lipases from the bacterium, despite the importance of understanding lipolysis and its impact on subsequent biohydrogenation of polyunsaturated fatty acids by rumen microbes. This study describes the draft genome of Anaerovibrio lipolytica 5ST, and the characterization of three lipolytic genes and their translated protein. The uncompleted draft genome was 2.83 Mbp and comprised of 2,673 coding sequences with a G+C content of 43.3%. Three putative lipase genes, alipA, alipB and alipC, encoding 492-, 438- and 248- amino acid peptides respectively, were identified using RAST. Phylogenetic analysis indicated that alipA and alipB clustered with the GDSL/SGNH family II, and alipC clustered with lipolytic enzymes from family V. Subsequent expression and purification of the enzymes showed that they were thermally unstable and had higher activities at neutral to alkaline pH. Substrate specificity assays indicated that the enzymes had higher hydrolytic activity against caprylate (C8), laurate (C12) and myristate (C14).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069076PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3741291PMC
March 2014

The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle.

PLoS One 2013 2;8(7):e67824. Epub 2013 Jul 2.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom.

It has been suggested that the ability of live yeast to improve milk yield and weight gain in cattle is because the yeast stimulates bacterial activity within the rumen. However it remains unclear if this is a general stimulation of all species or a specific stimulation of certain species. Here we characterised the change in the bacterial population within the rumen of cattle fed supplemental live yeast. Three cannulated lactating cows received a daily ration (24 kg/d) of corn silage (61% of DM), concentrates (30% of DM), dehydrated alfalfa (9% of DM) and a minerals and vitamins mix (1% of DM). The effect of yeast (BIOSAF SC 47, Lesaffre Feed Additives, France; 0.5 or 5 g/d) was compared to a control (no additive) in a 3 × 3 Latin square design. The variation in the rumen bacterial community between treatments was assessed using Serial Analysis of V1 Ribosomal Sequence Tag (SARST-V1) and 454 pyrosequencing based on analysis of the 16S rRNA gene. Compared to the control diet supplementation of probiotic yeast maintained a healthy fermentation in the rumen of lactating cattle (higher VFA concentration [high yeast dose only], higher rumen pH, and lower Eh and lactate). These improvements were accompanied with a shift in the main fibrolytic group (Fibrobacter and Ruminococcus) and lactate utilising bacteria (Megasphaera and Selenomonas). In addition we have shown that the analysis of short V1 region of 16s rRNA gene (50-60 bp) could give as much phylogenetic information as a longer read (454 pyrosequencing of 250 bp). This study also highlights the difficulty of drawing conclusions on composition and diversity of complex microbiota because of the variation caused by the use of different methods (sequencing technology and/or analysis).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067824PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699506PMC
February 2014

Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation.

J Nutr 2012 Sep 25;142(9):1684-92. Epub 2012 Jul 25.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK.

Balancing energy and nitrogen in the rumen is a key to both profitability and environmental sustainability. Four dairy cows were used in a Latin square experimental design to investigate the effect of severe nitrogen underfeeding (110 vs. 80% of requirements) and the type of carbohydrate consumed [neutral detergent fiber rich (FIB) vs. starch rich (STA)] on the rumen ecosystem. These dietary treatments modified both rumen fermentation and microbial populations. Compared with STA diets, consumption of FIB diets increased bacterial and fungal diversity in the rumen and also increased the concentrations of cellulolytic microorganisms, including protozoa (+38%), anaerobic fungi (+59%), and methanogens (+27%). This microbial adaptation to fiber utilization led to similar digestibility values for the 2 carbohydrate sources and was accompanied by a shift in the rumen fermentation patterns; when the FIB diets were consumed, the cows had greater ruminal pH, ammonia concentrations, and molar proportions of acetate and propionate compared with when they consumed the STA diets. Certain rumen microorganisms were sensitive to a shortage of nitrogen; rumen concentrations of ammonia were 49% lower when the low-protein (LP) diets were consumed as were total bacteria (-13%), anaerobic fungi (-28%), methanogens (-27%), protozoa (-19%), cellulolytic bacteria, and microbial diversity compared with when the high-protein (HP) diets were consumed. As a result, the digestibility of the LP diets was less than that of the HP diets. These findings demonstrated that the rumen microbial ecosystem is directly linked to the rumen fermentation pattern and, to some extent, to the efficiency of diet utilization by dairy cattle.
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http://dx.doi.org/10.3945/jn.112.159574DOI Listing
September 2012

As yet uncultured bacteria phylogenetically classified as Prevotella, Lachnospiraceae incertae sedis and unclassified Bacteroidales, Clostridiales and Ruminococcaceae may play a predominant role in ruminal biohydrogenation.

Environ Microbiol 2011 Jun 21;13(6):1500-12. Epub 2011 Mar 21.

Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, UK.

Microbial biohydrogenation of dietary poly-unsaturated fatty acids (PUFA) to saturated fatty acids (SFA) in the rumen results in the high ratio of SFA/PUFA in ruminant products, such as meat and milk. In vitro, Butyrivibrio proteoclasticus-related bacteria extensively biohydrogenate PUFA to SFA, yet their contribution in the rumen has not been confirmed. The aim of this study was to evaluate the role of Butyrivibrio proteoclasticus group bacteria in ruminal biohydrogenation and to assess the possible role of other bacteria. Fish oil at 0%, 1.5% and 3% dry matter intake was fed to eight Holstein × Friesian steers, in order to elicit changes in the extent of PUFA biohydrogenation. Fatty acid and B. proteoclasticus group 16S rRNA concentrations in rumen digesta were determined. Correlation between digesta 18:0 concentration and B. proteoclasticus group 16S rRNA concentration was low. Terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis (DGGE) coupled with multivariate statistics revealed that many terminal restriction fragments (T-RFs) and DGGE bands were linked to cis-9, trans-11 conjugated linoleic acid (CLA), 18:1 trans-11 and 18:0 ruminal concentrations. MiCA T-RF predictive identification software showed that these linked T-RFs were likely to originate from as yet uncultured bacteria classified as Prevotella, Lachnospiraceae incertae sedis, and unclassified Bacteroidales, Clostridiales and Ruminococcaceae. Sequencing of linked DGGE bands also revealed that as yet uncultured bacteria classified as Prevotella, Anaerovoax (member of the Lachnospiraceae incertae sedis family), and unclassified Clostridiales and Ruminococcaceae may play a role in biohydrogenation.
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http://dx.doi.org/10.1111/j.1462-2920.2011.02452.xDOI Listing
June 2011

The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs.

FEMS Microbiol Ecol 2010 May 16;72(2):272-8. Epub 2010 Feb 16.

Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystywth, UK.

The aim of this experiment was to study the persistence in time of bacterial and methanogenic archaeal communities that establish in the rumen of lambs fed two different diets at weaning. Twenty ewes with single lambs were used in two phases. In phase I, 10 lambs had access only to grass hay (H group). The other 10 lambs had free access to concentrate and grass hay (C group). After 20 weeks, five lambs from each group were slaughtered and rumen samples were kept for analysis. In phase II, the remaining lambs were grouped together and fed grass plus concentrate for 4 months and then slaughtered, and rumen samples were collected for analysis. Terminal restriction fragment length polymorphism analysis showed a different bacterial and methanogen population established in the rumen of H and C lambs in phase I. These differences disappeared for methanogens after both groups were fed the same diet for 4 months; however, the total bacterial community remained different for the H and C samples. Our results suggest that some of the differences in the microbial populations that establish in animals fed different diets at weaning persist in the long term, which provides the possibility of programming the microbial populations in the adult animal.
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http://dx.doi.org/10.1111/j.1574-6941.2010.00852.xDOI Listing
May 2010

Changes in the bacterial population of the caecum and stomach of the rabbit in response to addition of dietary caprylic acid.

Vet Microbiol 2010 Aug 28;144(3-4):334-9. Epub 2010 Jan 28.

Department of Animal Nutrition, Institute of Animal Science, Pratelstvi 815, 10401, Prague, Czech Republic.

The effect of caprylic acid, either in its pure form, or as Akomed R, on the microbial community of the stomach and caecum of farmed rabbits was investigated. This fatty acid, which is often added to the diet of farmed rabbits to reduce mortality rates was shown to reduce the number of coliforms isolated from both the stomach and the caecum. Moreover, it led to a reduction in the total number of anaerobic bacteria isolated from the caecum, but not for those isolated from the stomach. Its mode of action remains unclear, but here it is shown by use of both DGGE and TRFLP analysis that these changes are not confined to one specific group of bacteria, but rather affects a number of species.
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http://dx.doi.org/10.1016/j.vetmic.2010.01.013DOI Listing
August 2010