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Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms. Microorganisms 2022; 10:microorganisms10122345. [PMID: 36557598 PMCID: PMC9785684 DOI: 10.3390/microorganisms10122345] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022] Open
Abstract
As major structural components of plant cell walls, cellulose and hemicellulose are degraded and fermented by anaerobic microbes in the rumen to produce volatile fatty acids, the main nutrient source for the host. Cellulose degradation is carried out primarily by specialist bacteria, with additional contributions from protists and fungi, via a variety of mechanisms. Hemicelluloses are hydrolyzed by cellulolytic bacteria and by generalist, non-cellulolytic microbes, largely via extracellular enzymes. Cellulose hydrolysis follows first-order kinetics and its rate is limited by available substrate surface area. Nevertheless, its rate is at least an order of magnitude more rapid than in anaerobic digesters, due to near-obligatory adherence of microbial cells to the cellulose surface, and a lack of downstream inhibitory effects; in the host animal, fiber degradation rate is also enhanced by the unique process of rumination. Cellulolytic and hemicellulolytic microbes exhibit intense competition and amensalism, but they also display mutualistic interactions with microbes at other trophic levels. Collectively, the fiber-degrading community of the rumen displays functional redundancy, partial niche overlap, and convergence of catabolic pathways that all contribute to stability of the ruminal fermentation. The superior hydrolytic and fermentative capabilities of ruminal fiber degraders make them promising candidates for several fermentation technologies.
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Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen. Microorganisms 2022; 10:microorganisms10030551. [PMID: 35336126 PMCID: PMC8949432 DOI: 10.3390/microorganisms10030551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial peptides (AMPs) can efficiently control different microbial pathogens and show the potential to be applied in clinical practice and livestock production. In this work, the aim was to isolate AMP-producing ruminal streptococci and to characterize their genetic features through whole-genome sequencing. We cultured 463 bacterial isolates from the rumen of Nelore bulls, 81 of which were phenotypically classified as being Streptococcaceae. Five isolates with broad-range activity were genome sequenced and confirmed as being Streptococcus lutetiensis. The genetic features linked to their antimicrobial activity or adaptation to the rumen environment were characterized through comparative genomics. The genome of S. lutetiensis UFV80 harbored a putative CRISPR-Cas9 system (Type IIA). Computational tools were used to discover novel biosynthetic clusters linked to the production of bacteriocins. All bacterial genomes harbored genetic clusters related to the biosynthesis of class I and class II bacteriocins. SDS-PAGE confirmed the results obtained in silico and demonstrated that the class II bacteriocins predicted in the genomes of three S. lutetiensis strains had identical molecular mass (5197 Da). These results demonstrate that ruminal bacteria of the Streptococcus bovis/equinus complex represent a promising source of novel antimicrobial peptides.
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Xu Q, Qiao Q, Gao Y, Hou J, Hu M, Du Y, Zhao K, Li X. Gut Microbiota and Their Role in Health and Metabolic Disease of Dairy Cow. Front Nutr 2021; 8:701511. [PMID: 34422882 PMCID: PMC8371392 DOI: 10.3389/fnut.2021.701511] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ruminants are mostly herbivorous animals that employ rumen fermentation for the digestion of feed materials, including dairy cows. Ruminants consume plant fibre as their regular diet, but lack the machinery for their digestion. For this reason, ruminants maintain a symbiotic relation with microorganisms that are capable of producing enzymes to degrade plant polymers. Various species of microflora including bacteria, protozoa, fungi, archaea, and bacteriophages are hosted at distinct concentrations for accomplishing complete digestion. The ingested feed is digested at a defined stratum. The polysaccharic plant fibrils are degraded by cellulolytic bacteria, and the substrate formed is acted upon by other bacteria. This sequential degradative mechanism forms the base of complete digestion as well as harvesting energy from the ingested feed. The composition of microbiota readily gets tuned to the changes in the feed habits of the dairy cow. The overall energy production as well as digestion is decided by the intactness of the resident communal flora. Disturbances in the homogeneity gastrointestinal microflora has severe effects on the digestive system and various other organs. This disharmony in communal relationship also causes various metabolic disorders. The dominance of methanogens sometimes lead to bloating, and high sugar feed culminates in ruminal acidosis. Likewise, disruptive microfloral constitution also ignites reticuloperitonitis, ulcers, diarrhoea, etc. The role of symbiotic microflora in the occurrence and progress of a few important metabolic diseases are discussed in this review. Future studies in multiomics provides platform to determine the physiological and phenotypical upgradation of dairy cow for milk production.
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Affiliation(s)
- Qingbiao Xu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qinqin Qiao
- College of Information Engineering, Fuyang Normal University, Fuyang, China
| | - Ya Gao
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinxiu Hou
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mingyang Hu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yufeng Du
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ke Zhao
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiang Li
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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Huo W, Wang X, Wei Z, Zhang H, Liu Q, Zhang S, Wang C, Chen L, Xu Q, Guo G. Effect of lactic acid bacteria on the ensiling characteristics and in vitro ruminal fermentation parameters of alfalfa silage. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1906167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Wenjie Huo
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Xinyu Wang
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Zhixia Wei
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Haixuan Zhang
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Qiang Liu
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Shuanlin Zhang
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Cong Wang
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Lei Chen
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Qingfang Xu
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
| | - Gang Guo
- Animal Sciences College, Shanxi Agricultural University, Jinzhong, China
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Yeoman CJ, Fields CJ, Lepercq P, Ruiz P, Forano E, White BA, Mosoni P. In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses. mBio 2021; 12:e03533-20. [PMID: 33658330 PMCID: PMC8092306 DOI: 10.1128/mbio.03533-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens are the three predominant cellulolytic bacterial species found in the rumen. In vitro studies have shown that these species compete for adherence to, and growth upon, cellulosic biomass. Yet their molecular interactions in vivo have not heretofore been examined. Gnotobiotically raised lambs harboring a 17-h-old immature microbiota devoid of culturable cellulolytic bacteria and methanogens were inoculated first with F. succinogenes S85 and Methanobrevibacter sp. strain 87.7, and 5 months later, the lambs were inoculated with R. albus 8 and R. flavefaciens FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, in sacco fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that F. succinogenes establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in an increase in carboxymethyl cellulase (CMCase) and xylanase activities but not in greater fibrolysis, suggesting that F. succinogenes and ruminococci deploy different but equally effective means to degrade plant cell walls. Expression profiles showed that F. succinogenes relied upon outer membrane vesicles and a diverse repertoire of CAZymes, while R. albus and R. flavefaciens preferred type IV pili and either CBM37-harboring or cellulosomal carbohydrate-active enzymes (CAZymes), respectively. The changes in cellulolytics also affected the rumen metabolome, including an increase in acetate and butyrate at the expense of propionate. In conclusion, this study provides the first demonstration of in vivo competition between the three predominant cellulolytic bacteria and provides insight on the influence of these ecological interactions on rumen fibrolytic function and metabolomic response.IMPORTANCE Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens, has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production. This study provides the first evidence of in vivo competitions between F. succinogenes and the two Ruminococcus species. It shows that a simple disequilibrium within the cellulolytic community has repercussions on the rumen metabolome and fermentation end products. This finding will have to be considered in the future when determining strategies aiming at directing rumen fermentations for animal production.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | - Christopher J Fields
- Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Pascale Lepercq
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
| | - Pascale Mosoni
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
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Sabino YNV, de Araújo KC, de Assis FGDV, Moreira SM, Lopes TDS, Mendes TADO, Huws SA, Mantovani HC. In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides. Front Microbiol 2020; 11:576738. [PMID: 33072042 PMCID: PMC7533575 DOI: 10.3389/fmicb.2020.576738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.
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Affiliation(s)
| | | | | | | | | | | | - Sharon Ann Huws
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, United Kingdom
| | - Hilário C Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Brazil
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Li Y, Rebuffat S. The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology. J Biol Chem 2020; 295:34-54. [PMID: 31784450 PMCID: PMC6952617 DOI: 10.1074/jbc.rev119.006545] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
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8
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Bovicins: The Bacteriocins of Streptococci and Their Potential in Methane Mitigation. Probiotics Antimicrob Proteins 2019; 11:1403-1413. [DOI: 10.1007/s12602-018-9502-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Harlow BE, Flythe MD, Aiken GE. Effect of biochanin A on corn grain (Zea mays) fermentation by bovine rumen amylolytic bacteria. J Appl Microbiol 2017; 122:870-880. [PMID: 28055130 DOI: 10.1111/jam.13397] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/27/2016] [Accepted: 01/02/2017] [Indexed: 02/01/2023]
Abstract
AIMS The objective was to determine the effect of biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense L.), on corn fermentation by rumen micro-organisms. METHODS AND RESULTS When bovine rumen bacterial cell suspensions (n = 3) were incubated (24 h, 39°C) with ground corn, amylolytic bacteria including group D Gram-positive cocci (GPC; Streptococcus bovis; enterococci) proliferated, cellulolytic bacteria were inhibited, lactate accumulated and pH declined. Addition of BCA (30 μg ml-1 ) inhibited lactate production, and pH decline. BCA had no effect on total amylolytics, but increased lactobacilli and decreased GPC. The initial rate and total starch disappearance was decreased by BCA addition. BCA with added Strep. bovis HC5 supernatant (containing bacteriocins) inhibited the amylolytic bacteria tested (Strep. bovis JB1; Strep. bovis HC5; Lactobacillus reuteri, Selenemonas ruminatium) to a greater extent than either addition alone. BCA increased cellulolytics and dry matter digestibility of hay with corn starch. CONCLUSIONS These results indicate that BCA mitigates changes associated with corn fermentation by bovine rumen bacteria ex vivo. SIGNIFICANCE AND IMPACT OF THE STUDY BCA could serve as an effective mitigation strategy for rumen acidosis. Future research is needed to evaluate the effect of BCA on mitigating rumen acidosis in vivo.
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Affiliation(s)
- B E Harlow
- Forage-Animal Production Research Unit, USDA, Agricultural Research Service, Lexington, KY, USA
| | - M D Flythe
- Forage-Animal Production Research Unit, USDA, Agricultural Research Service, Lexington, KY, USA
| | - G E Aiken
- Forage-Animal Production Research Unit, USDA, Agricultural Research Service, Lexington, KY, USA
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Oss DB, Ribeiro GO, Marcondes MI, Yang W, Beauchemin KA, Forster RJ, McAllister TA. Synergism of Cattle and Bison Inoculum on Ruminal Fermentation and Select Bacterial Communities in an Artificial Rumen (Rusitec) Fed a Barley Straw Based Diet. Front Microbiol 2016; 7:2032. [PMID: 28018336 PMCID: PMC5156676 DOI: 10.3389/fmicb.2016.02032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the effect of increasing the proportion of bison relative to cattle inoculum on fermentation and microbial populations within an artificial rumen (Rusitec). The experiment was a completely randomized design with a factorial treatment structure (proportion cattle:bison inoculum; 0:100, 33:67, 67:33, and 100:0) replicated in two Rusitec apparatuses (n = 8 fermenters). The experiment was 15 d with 8 d of adaptation and 7 d of sampling. Fermenters were fed a diet of 70:30 barley straw:concentrate (DM basis). True digestibility of DM was determined after 48 h of incubation from d 13 to 15, and daily ammonia (NH3) and volatile fatty acid (VFA) production were measured on d 9–12. Protozoa counts were determined at d 9, 11, 13, and 15 and particle-associated bacteria (PAB) from d 13 to 15. Select bacterial populations in the PAB were measured using RT-qPCR. Fermenter was considered the experimental unit and day of sampling as a repeated measure. Increasing the proportion of bison inoculum resulted in a quadratic effect (P < 0.05) on straw, concentrate and total true DM disappearance and on straw and total neutral detergent fiber (aNDF) disappearance, with greater disappearances observed with mixed inoculum. There were no effect of source or proportion of inoculum on ADF disappearance (P > 0.05). Increasing bison inoculum linearly increased (P < 0.05) concentrate aNDF disappearance, total and concentrate N disappearance as well as total daily VFA and acetate production. A positive quadratic response (P < 0.05) was observed for daily NH3-N, propionate, butyrate, valerate, isovalerate and isobutyrate production, as well as the acetate:propionate ratio. Increasing the proportion of bison inoculum linearly increased (P < 0.05) total protozoa numbers. No effects were observed on pH, total gas and methane production, microbial N synthesis, or copies of 16S rRNA associated with total bacteria, Selenomonas ruminantium or Prevotella bryantii. Increasing bison inoculum had a quadratic effect (P < 0.05) on Fibrobacter succinogenes, and tended to linearly (P < 0.10) increase Ruminococcus flavefaciens and decrease (P < 0.05) Ruminococcus albus copy numbers. In conclusion, bison inoculum increased the degradation of feed protein and fiber. A mixture of cattle and bison rumen inoculum acted synergistically, increasing the DM and aNDF disappearance of barley straw.
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Affiliation(s)
- Daniela B Oss
- Departamento de Zootecnia, Universidade Federal de ViçosaViçosa, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Ministério da EducaçãoBrasília, Brazil
| | - Gabriel O Ribeiro
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Ministério da EducaçãoBrasília, Brazil; Lethbridge Research and Development Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Marcos I Marcondes
- Departamento de Zootecnia, Universidade Federal de Viçosa Viçosa, Brazil
| | - WenZhu Yang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - Karen A Beauchemin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - Robert J Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
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Krause DO, Nagaraja TG, Wright ADG, Callaway TR. Board-invited review: Rumen microbiology: leading the way in microbial ecology. J Anim Sci 2013; 91:331-41. [PMID: 23404990 DOI: 10.2527/jas.2012-5567] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.
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Affiliation(s)
- D O Krause
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Hsieh YH, Wang HT, Hsu JT, Chen CY. Albusin B, mass-produced by the Saccharomyces cerevisiae suppression system, enhances lipid utilisation and antioxidant capacity in mice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:2758-2764. [PMID: 23553112 DOI: 10.1002/jsfa.6095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 01/14/2013] [Accepted: 02/07/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Albusin B (bacteriocin), isolated from Ruminococcus albus 7 and mass-produced by the Saccharomyces cerevisiae expression system, has previously been shown to have a beneficial effect on lipid metabolism in broiler chickens. The present study was focused on the effect of albusin B on lipid metabolism in mice and the potential of albusin B-expressing yeast product (albusin B) as a food supplement. Forty-five BALB/c male mice at 6 weeks of age were each orally administered normal saline (control), yeast (0.125 mg kg(-1) ) or albusin B (0.125 mg kg(-1) ) for 14 days and then euthanised. RESULTS Compared with the control group, albusin B-fed mice exhibited decreased body weight and plasma levels of triglycerides and free fatty acids but increased plasma high-density lipoprotein. Albusin B-fed mice showed higher mRNA expression of fatty acid oxidation in the ileum, heart and liver than control mice. Compared with the control treatment, both yeast and albusin B treatments caused a decrease in mRNA expression of fatty acid synthesis in the heart and liver. Moreover, albusin B suppressed mRNA levels of lipogenesis in the ileum and liver. Albusin B-fed mice exhibited more favourable adenosine triphosphate production and antioxidant capacity in the heart and liver. Albusin B treatment led to a significantly lower respiratory quotient than that of the control, whereas yeast treatment did not. CONCLUSION This study demonstrated a beneficial effect of albusin B on lipid utilisation and anti-atherosclerotic and antioxidant capacities in mice. However, more comprehensive studies are required to elucidate the exact mechanism behind the effect of albusin B.
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Affiliation(s)
- Ya-Hui Hsieh
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec. 3, Keelung Rd, Taipei, Taiwan
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The influence of environmental factors on the adhesion of combinations of probiotics to rice fibre fractions. World J Microbiol Biotechnol 2012; 28:2293-302. [DOI: 10.1007/s11274-012-1035-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
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14
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Production and characterization of a bacteriocin from ruminal bacterium Ruminococcus albus 7. Biosci Biotechnol Biochem 2012; 76:34-41. [PMID: 22232237 DOI: 10.1271/bbb.110348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The characteristics of a bacteriocin from Ruminococcus albus 7 and its potential as an antibiotic alternative were examined in this study. The addition of 3 µM 3-phenylpropanoic acid (PPA) and 0.2% Tween 80 to the culturing medium improved bacteriocin production by 2.5-fold. Native polyacrylamide gel electrophoresis of the antagonistically active gel filtration fraction established that the molecular weight of the R. albus 7 bacteriocin was approximately 36 kDa. The bacteriocin was sensitive to pepsin, protease, and pancreatin, and was inactivated by heating at 65 °C for 1 h. Simulating in vitro avian digestion decreased the antagonistic activity by 74.7%, but the addition of 1% bovin serum albumin restored 13% of the lost antagonistic activity. Following ion-exchange purification, the bacteriocin had sufficient antagonistic activity against five tested pathogenic strains, but the addition of a protectant is necessary for utilization of bacteriocin of R. albus 7 as an antibiotic alternative in animal feed.
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Fiber digestion, VFA production, and microbial population changes during in vitro ruminal fermentations of mixed rations by monensin-adapted and unadapted microbes. Anim Feed Sci Technol 2011. [DOI: 10.1016/j.anifeedsci.2011.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Wang HT, Yu C, Hsieh YH, Chen SW, Chen BJ, Chen CY. Effects of albusin B (a bacteriocin) of Ruminococcus albus 7 expressed by yeast on growth performance and intestinal absorption of broiler chickens--its potential role as an alternative to feed antibiotics. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2011; 91:2338-2343. [PMID: 21567416 DOI: 10.1002/jsfa.4463] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/14/2010] [Accepted: 04/07/2011] [Indexed: 05/30/2023]
Abstract
BACKGROUND Bacteriocins with antimicrobial activity are considered as potential alternatives to antibiotics. The aim of this study was to investigate the effect of albusin B (bacteriocin) of Ruminococcus albus 7 expressed by yeast on the growth performance of broiler chickens. Ninety 1-day-old healthy broiler chickens were randomly divided into three groups: control, albusin B (2.5 g kg(-1)) and nosiheptide (2.5 mg kg(-1), antibiotic control). Growth performance and intestinal functions were measured at 5 weeks of age. RESULTS Albusin B-supplemented broilers showed increased body weight gain compared with control broilers (54.7 ± 5.3 vs 48.5 ± 6.1 g day(-1) per bird, P < 0.05). Broilers supplemented with nosiheptide had a less developed mucosal layer than broilers in the other two groups. Compared with the control group, broilers supplemented with albusin B or nosiheptide showed increased mRNA expression of sGLT1, GLUT2 and PEPT1 in the jejunum (P < 0.05). The faecal Lactobacillus count was higher in the albusin B group than in the other two groups (P < 0.05). CONCLUSION Albusin B supplementation increased intestinal absorption and elevated the faecal Lactobacillus count, thereby promoting the growth performance of broiler chickens. These improvements resulting from albusin B supplementation provide evidence of potential alternatives to antibiotics in broiler chicken feed.
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Affiliation(s)
- Han-Tsung Wang
- Department of Animal Science, Chinese Culture University, Taipei, Taiwan
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McAllister TA, Beauchemin KA, Alazzeh AY, Baah J, Teather RM, Stanford K. Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2011. [DOI: 10.4141/cjas10047] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
McAllister, T. A., Beauchemin, K. A., Alazzeh, A. Y., Baah, J., Teather, R. M. and Stanford, K. 2011. Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle. Can. J. Anim. Sci. 91: 193–211. Direct-fed microbials (DFM) have been employed in ruminant production for over 30 yr. Originally, DFM were used primarily in young ruminants to accelerate establishment of the intestinal microflora involved in feed digestion and to promote gut health. Further advancements led to more sophisticated mixtures of DFM that are targeted at improving fiber digestion and preventing ruminal acidosis in mature cattle. Through these outcomes on fiber digestion/rumen health, second-generation DFM have also resulted in improvements in milk yield, growth and feed efficiency of cattle, but results have been inconsistent. More recently, there has been an emphasis on the development of DFM that exhibit activity in cattle against potentially zoonotic pathogens such as Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus. Regulatory requirements have limited the microbial species within DFM products to organisms that are generally recognized as safe, such as lactic acid-producing bacteria (e.g., Lactobacillus and Enterococcus spp.), fungi (e.g., Aspergillus oryzae), or yeast (e.g., Saccharomyces cerevisiae). Direct-fed microbials of rumen origin, involving lactate-utilizing species (e.g., Megasphaera elsdenii, Selenomonas ruminantium, Propionibacterium spp.) and plant cell wall-degrading isolates of Butyrivibrio fibrisolvens have also been explored, but have not been commercially used. Development of DFM that are efficacious over a wide range of ruminant production systems remains challenging because[0] comprehensive knowledge of microbial ecology is lacking. Few studies have employed molecular techniques to study in detail the interaction of DFM with native microbial communities or the ruminant host. Advancements in the metagenomics of microbial communities and the genomics of microbial–host interactions may enable DFM to be formulated to improve production and promote health, responses that are presently often achieved through the use of antimicrobials in cattle.
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Affiliation(s)
- T. A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada T1J 4B1
| | - K. A. Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada T1J 4B1
| | - A. Y. Alazzeh
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada T1J 4B1
| | - J. Baah
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada T1J 4B1
| | - R. M. Teather
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada T1J 4B1
| | - K. Stanford
- Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (e-mail: )
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Belanche A, Balcells J, De La Fuente G, Yañez-Ruíz DR, Fondevila M, Calleja L. ORIGINAL ARTICLE: Description of development of rumen ecosystem by PCR assay in milk-fed, weaned and finished lambs in an intensive fattening system. J Anim Physiol Anim Nutr (Berl) 2010; 94:648-58. [DOI: 10.1111/j.1439-0396.2009.00952.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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An rRNA-based analysis for evaluating the effect of heat stress on the rumen microbial composition of Holstein heifers. Anaerobe 2010; 16:27-33. [DOI: 10.1016/j.anaerobe.2009.04.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 04/21/2009] [Accepted: 04/29/2009] [Indexed: 11/22/2022]
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20
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Composition of the landfill microbial community as determined by application of domain- and group-specific 16S and 18S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 2009; 76:1301-6. [PMID: 20023104 DOI: 10.1128/aem.01783-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbial community composition of colonized cotton and leachate samples from a landfill was quantified using small subunit (SSU) rRNA probes (quantitative rRNA hybridization). Relative quantification of bacteria, eukaryotes, and archaea revealed variations in the landfill microbial community between samples from different areas of the landfill site and indicated the presence of potentially novel archaea. Anaerobic fungi were quantified in rumen fluid samples but were not sufficiently abundant for direct detection in the landfill samples.
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Cookson AL, Noel SJ, Kelly WJ, Attwood GT. The use of PCR for the identification and characterisation of bacteriocin genes from bacterial strains isolated from rumen or caecal contents of cattle and sheep. FEMS Microbiol Ecol 2009; 48:199-207. [PMID: 19712403 DOI: 10.1016/j.femsec.2004.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
PCR primers were designed to amplify the gene that encodes bovicin 255 from Streptococcus gallolyticus LRC0255 and the bacteriocin genes from Butyrivibrio fibrisolvens strains AR10 and OR79A (bviD and bvi79A) in order to screen for their incidence in rumen and caecal B. fibrisolvens and Streptococcus bovis-like isolates from New Zealand and North American ruminants. None of the B. fibrisolvens-like strains (n=34) isolated from New Zealand or North America had the genes encoding for butyrivibriocins AR10 (bviD) or OR79 (bvi79A). However, seven S. bovis isolates from New Zealand ruminants and three from North American animals had the bovicin 255 gene. Sequence comparison of cloned bovicin 255 PCR products indicated a 92.9-95.7% similarity to that of the corresponding bovicin 255 gene sequence of S. gallolyticus. Four of the New Zealand bovicin 255 positive S. bovis isolates were from the caecal contents of the same sheep and had identical PFGE profiles. Two other S. bovis isolates sharing the same PFGE profile were isolated from a separate animal from the same flock. PFGE analysis of the North American strains indicated that all three were closely related as two of three had identical PFGE profiles with the remaining isolate differing only by a single band position. The 16S rRNA gene sequences of the 10 isolates were at least 99.8% identical to S. bovis. All 10 S. bovis isolates having the gene for bovicin 255 produced bacteriocin activity that inhibited the growth of Peptostreptococcus anaerobius D1 in a deferred antagonism plating (DAP) assay. Certain S. bovis isolates obtained from ruminants have bacteriocin activity associated with a distinct bovicin 255 gene sequence but it appears that bacteriocin production by the rumen anaerobe B. fibrisolvens may be uncommon in strains isolated from cattle and sheep in New Zealand.
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Affiliation(s)
- Adrian L Cookson
- Rumen Microbial Functional Genomics, Nutrition and Behaviour Group, AgResearch, Grasslands Research Centre, Tennent Drive, Palmerston North, New Zealand.
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Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 2009; 4:e6650. [PMID: 19680555 PMCID: PMC2721979 DOI: 10.1371/journal.pone.0006650] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 07/07/2009] [Indexed: 11/19/2022] Open
Abstract
Background Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. Methodology/Principal Findings The R. flavefaciens FD-1 genome was sequenced to 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs), polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated, 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of up-regulation. Conclusions/Significance The genomic evidence indicates that R. flavefaciens FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a cellulosome architecture. Functional analysis of the genome has revealed that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.
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Affiliation(s)
- Margret E. Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Dionysios A. Antonopoulos
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Marco T. Rincon
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Mark Band
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Albert Bari
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Tatsiana Akraiko
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alvaro Hernandez
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jyothi Thimmapuram
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, Marseille, France
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Harry J. Flint
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bryan A. White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Bennegadi N, Fonty G, Millet L, Gidenne T, Licois D. Effects of Age and Dietary Fibre Level on Caecal Microbial Communities of Conventional and Specific Pathogen-Free Rabbits. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.1080/08910600310015574] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Nadia Bennegadi
- Station de Recherches Cunicoles INRA CR Toulouse, BP 27 31326 Castanet-Tolosan
| | - Gérard Fonty
- Laboratoire de Microbiologie INRA CR Clermont-Ferrand, Theix 63122 Saint-Genès-Champanelle
| | - Liliane Millet
- Laboratoire de Microbiologie INRA CR Clermont-Ferrand, Theix 63122 Saint-Genès-Champanelle
| | - Thierry Gidenne
- Station de Recherches Cunicoles INRA CR Toulouse, BP 27 31326 Castanet-Tolosan
| | - Dominique Licois
- Laboratoire de Pathologie du Lapin Station de Pathologie Aviaire et de Parasitologie, INRA CR Tours 37380 Nouzilly
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Uyeno Y, Sekiguchi Y, Tajima K, Takenaka A, Kurihara M, Kamagata Y. Evaluation of group-specific, 16S rRNA-targeted scissor probes for quantitative detection of predominant bacterial populations in dairy cattle rumen. J Appl Microbiol 2008; 103:1995-2005. [PMID: 17953610 DOI: 10.1111/j.1365-2672.2007.03443.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To develop a suite of group-specific, rRNA-targeted oligonucleotide scissor probes for the quantitative detection of the predominant bacterial groups within the ruminal microbial community with the rRNA cleavage reaction-mediated microbial quantification method. METHODS AND RESULTS Oligonucleotides that complement the conserved sites of the 16S rRNA of phylogenetically defined groups of bacteria that significantly contribute to the anaerobic fermentation of carbohydrates in ruminal ecosystems were selected from among published probes or were newly designed. For each probe, target-specific rRNA cleavage was achieved by optimizing the formamide concentration in the reaction mixture. The set of scissor probes was then used to analyse the bacterial community in the rumen fluids of four healthy dairy cows. In the rumen fluid samples, the genera Bacteroides/Prevotella and Fibrobacter and the Clostridium coccoides-Eubacterium rectale group were detected in abundance, accounting for 44-48%, 2.9-10%, and 9.1-10% of the total 16S rRNA, respectively. The coverage with the probe set was 71-78% of the total bacterial 16S rRNA. CONCLUSIONS The probe set coupled with the sequence-specific small-subunit rRNA cleavage method can be used to analyse the structure of a ruminal bacterial community. SIGNIFICANCE AND IMPACT OF THE STUDY The probe set developed in this study provides a tool for comprehensive rRNA-based monitoring of the community members that dominate ruminal ecosystems. As the ruminal microbial community can be perturbed, it is important to track its dynamics by analysing microbiological profiles under specific conditions. The method described here will provide a convenient approach for such tracking.
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Affiliation(s)
- Y Uyeno
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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25
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Nikolaev YA, Plakunov VK. Biofilm—“City of microbes” or an analogue of multicellular organisms? Microbiology (Reading) 2007. [DOI: 10.1134/s0026261707020014] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Gough JM, Conlan LL, Denman SE, Krause DO, Smith WJM, Williamson MA, McSweeney CS. Screening of bacteria from the cattle gastrointestinal tract for inhibitory activity against enterohemorrhagic Escherichia coli O157:H7, O111:H-, and O26:H11. J Food Prot 2006; 69:2843-50. [PMID: 17186648 DOI: 10.4315/0362-028x-69.12.2843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A quick and reproducible microgel plate assay was adapted to screen bacteria from cattle gastrointestinal tracts for production of compounds inhibitory to the growth of three enterohemorrhagic Escherichia coli (EHEC) serotypes: O157:H7, O111:H-, and O26:H11. The inhibitory activity of 309 bacteria, isolated on several agar media, was assessed by a microgel assay performed in 96-well microtiter plates. Fifty-three isolates secreted inhibitory compounds with a molecular weight of less than 1,000. In 12 isolates, the inhibitory activity was attributable to compounds other than lactic or acetic acid. These compounds were highly heat tolerant, with varying sensitivity to digestion by proteolytic enzymes. The inhibitory isolates were identified as lactic acid-producing bacteria on the basis of a combination of analyses, including 16S-rDNA restriction fragment length polymorphisms, 16S-rDNA gene sequences, and fermentation end products. The lactic acid bacteria of ruminants may contain antibacterial compounds not yet described. Naturally occurring populations of lactic acid bacteria may have potential as probiotics, to reduce the carriage of EHEC in the gastrointestinal tract of ruminants.
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Affiliation(s)
- J M Gough
- Commonwealth Scientific and Industrial Research Organisation (C.S.I.R.O.) Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
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27
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Wells JE, Krause DO, Callaway TR, Russell JB. A bacteriocin-mediated antagonism by ruminal lactobacilli against Streptococcus bovis. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00376.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Chen J, Stevenson DM, Weimer PJ. Albusin B, a bacteriocin from the ruminal bacterium Ruminococcus albus 7 that inhibits growth of Ruminococcus flavefaciens. Appl Environ Microbiol 2004; 70:3167-70. [PMID: 15128585 PMCID: PMC404437 DOI: 10.1128/aem.70.5.3167-3170.2004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An approximately 32-kDa protein (albusin B) that inhibited growth of Ruminococcus flavefaciens FD-1 was isolated from culture supernatants of Ruminococcus albus 7. Traditional cloning and gene-walking PCR techniques revealed an open reading frame (albB) encoding a protein with a predicted molecular mass of 32,168 Da. A BLAST search revealed two homologs of AlbB from the unfinished genome of R. albus 8 and moderate similarity to LlpA, a recently described 30-kDa bacteriocin from Pseudomonas sp. strain BW11M1.
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Affiliation(s)
- Junqin Chen
- Department of Bacteriology, University of Wisconsin-Madison, USA
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Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS. Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 2003; 27:663-93. [PMID: 14638418 DOI: 10.1016/s0168-6445(03)00072-x] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.
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Affiliation(s)
- Denis O Krause
- CSIRO Australia, Queensland Bioscience Precinct, St. Lucia, Qld 4067, Australia.
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Parret AHA, Schoofs G, Proost P, De Mot R. Plant lectin-like bacteriocin from a rhizosphere-colonizing Pseudomonas isolate. J Bacteriol 2003; 185:897-908. [PMID: 12533465 PMCID: PMC142807 DOI: 10.1128/jb.185.3.897-908.2003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2002] [Accepted: 11/06/2002] [Indexed: 11/20/2022] Open
Abstract
Rhizosphere isolate Pseudomonas sp. strain BW11M1, which belongs to the Pseudomonas putida cluster, secretes a heat- and protease-sensitive bacteriocin which kills P. putida GR12-2R3. The production of this bacteriocin is enhanced by DNA-damaging treatment of producer cells. We isolated a TnMod mutant of strain BW11M1 that had lost the capacity to inhibit the growth of strain GR12-2R3. A wild-type genomic fragment encompassing the transposon insertion site was shown to confer the bacteriocin phenotype when it was introduced into Escherichia coli cells. The bacteriocin structural gene was identified by defining the minimal region required for expression in E. coli. This gene was designated llpA (lectin-like putidacin) on the basis of significant homology of its 276-amino-acid product with mannose-binding lectins from monocotyledonous plants. LlpA is composed of two monocot mannose-binding lectin (MMBL) domains. Several uncharacterized bacterial genes encoding diverse proteins containing one or two MMBL domains were identified. A phylogenetic analysis of the MMBL domains present in eukaryotic and prokaryotic proteins assigned the putidacin domains to a new bacterial clade within the MMBL-containing protein family. Heterologous expression of the llpA gene also conveyed bacteriocin production to several Pseudomonas fluorescens strains. In addition, we demonstrated that strain BW11M1 and heterologous hosts secrete LlpA into the growth medium without requiring a cleavable signal sequence. Most likely, the mode of action of this lectin-like bacteriocin is different from the modes of action of previously described Pseudomonas bacteriocins.
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Affiliation(s)
- Annabel H A Parret
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium.
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KOBAYASHI Y, YAMAMOTO M. Factors that limit maintenance of recombinant rumen bacterium in sheep rumen. Anim Sci J 2002. [DOI: 10.1046/j.1344-3941.2002.00019.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rychlik JL, Russell JB. Bacteriocin-like activity of Butyrivibrio fibrisolvens JL5 and its effect on other ruminal bacteria and ammonia production. Appl Environ Microbiol 2002; 68:1040-6. [PMID: 11872448 PMCID: PMC123762 DOI: 10.1128/aem.68.3.1040-1046.2002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When ruminal bacteria from a cow fed hay were serially diluted into an anaerobic medium that had only peptides and amino acids as energy sources, little growth or ammonia production was detected at dilutions greater than 10(-6). The 10(-8) and 10(-9) dilutions contained bacteria that fermented carbohydrates, and some of these bacteria inhibited Clostridium sticklandii SR, an obligate amino acid-fermenting bacterium. Phylogenetic analysis indicated that the most active isolate (JL5) was closely related to Butyrivibrio fibrisolvens B835. Strain JL5 inhibited B. fibrisolvens 49 and a variety of other gram-positive organisms, but it had little effect on most gram-negative ruminal bacteria. Strain JL5 did not produce a bacteriocin-like inhibitory substance (BLIS) until it reached the late log or stationary phase. The JL5 BLIS did not cause the lysis of B. fibrisolvens 49, but the intracellular potassium level, the ATP level, the electrical potential, and the viability decreased rapidly. The JL5 BLIS also caused marked decreases in the viability and cellular potassium level of C. sticklandii SR. The membrane potential and intracellular ATP level also declined. The BLIS was degraded very slowly by pronase E, but it could be precipitated with 60% ammonium sulfate and dialyzed (3,500-Da cutoff). The BLIS could be separated from other peptides by polyacrylamide gel electrophoresis, and C. sticklandii SR overlays indicated that the molecular size of this compound was approximately 3,600 Da. Based on these results, it appeared that the JL5 BLIS was a pore-forming peptide. Because carbohydrate-fermenting ruminal bacteria could inhibit the growth of obligate amino acid-fermenting bacteria, BLIS may play a role in regulating ammonia production in vivo.
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Affiliation(s)
- Jennifer L Rychlik
- Section of Microbiology, Cornell University, Ithaca, New York 14853, USA
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Morovský M, Pristas P, Javorský P, Nes IF, Holo H. Isolation and characterization of enterocin BC25 and occurrence of the entA gene among ruminal gram-positive cocci. Microbiol Res 2002; 156:133-8. [PMID: 11572452 DOI: 10.1078/0944-5013-00090] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Enterocin BC25, a bacteriocin produced by Enterococcus faecium BC25 isolated from the rumen of cow was purified to homogeneity and sequenced. Twenty amino acids were identified in the peptide chain (TTHSGKYYGNGVYCT-KNKCT), identical to the N-terminal sequence of enterocin A. The DNA sequence of the enterocin BC25 structural gene and putative immunity protein exhibited high similarity to the entA gene. The occurrence of a 726 bp amplicon containing the enterocin A structural gene was studied among gram-positive ruminal cocci by PCR. Our results showed wide occurrence of the entA structural gene among ruminal enterococcal and streptococcal bacterial strains tested, and indicate variable ability to express bacteriocin production and resistance.
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Affiliation(s)
- M Morovský
- Department of Biochemistry, Faculty of Science, P. J. Safárik University, Kosice, Slovakia
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Koike S, Kobayashi Y. Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol Lett 2001; 204:361-6. [PMID: 11731149 DOI: 10.1111/j.1574-6968.2001.tb10911.x] [Citation(s) in RCA: 297] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Competitive PCR assays were developed for the enumeration of the rumen cellulolytic bacterial species: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. The assays, targeting species-specific regions of 16S rDNA, were evaluated using DNA from pure culture and rumen digesta spiked with the relevant cellulolytic species. Minimum detection levels for F. succinogenes, R. albus and R. flavefaciens were 1-10 cells in pure culture and 10(3-4) cells per ml in mixed culture. The assays were reproducible and 11-13% inter- and intra-assay variations were observed. Enumeration of the cellulolytic species in the rumen and alimentary tract of sheep found F. succinogenes dominant (10(7) per ml of rumen digesta) compared to the Ruminococcus spp. (10(4-6) per ml). The population size of the three species did not change after the proportion of dietary alfalfa hay was increased. All three species were detected in the rumen, omasum, caecum, colon and rectum. Numbers of the cellulolytic species at these sites varied within and between animals.
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Affiliation(s)
- S Koike
- Graduate School of Agriculture, Hokkaido University, 060-8589, Sapporo, Japan
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35
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Krause DO, Bunch RJ, Conlan LL, Kennedy PM, Smith WJ, Mackie RI, McSweeney CS. Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1719-1729. [PMID: 11429450 DOI: 10.1099/00221287-147-7-1719] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Digestibility of fibre in ruminants may be improved by the introduction of highly fibrolytic strains of ruminal bacteria. This approach may be feasible if, for example, strains of Ruminococcus that are significantly more fibrolytic than the normal population of Ruminococcus are used for inoculation purposes. Introduced strains of bacteria, irrespective of ecosystem, often decline after inoculation, and in this study, highly fibrolytic strains of Ruminococcus were continuously dosed to ensure that measurements of fibre digestion were made in the presence of significant numbers of the introduced bacteria. During dosing the total culturable count increased significantly (P<0.05), but declined post-dosing. The level of dosed Ruminococcus, and total Ruminococcus, Fibrobacter succinogenes and eukaryotes measured by 16S rRNA probes increased significantly (P<0.05) during the dosing period, but also declined post-dosing. When in vitro nylon bag digestibility, feed intake or whole-tract digestibility was measured, no improvement could be measured.
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Affiliation(s)
- Denis O Krause
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Brisbane, Qld 4068, Australia1
| | - Rowan J Bunch
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Brisbane, Qld 4068, Australia1
| | - Lawrence L Conlan
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Brisbane, Qld 4068, Australia1
| | - Peter M Kennedy
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Brisbane, Qld 4068, Australia1
| | - Wendy J Smith
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Brisbane, Qld 4068, Australia1
| | - Roderick I Mackie
- Department of Animal Sciences, University of Illinios, Urbana, IL, USA2
| | - Christopher S McSweeney
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Brisbane, Qld 4068, Australia1
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Krause DO, Bunch RJ, Dalrymple BD, Gobius KS, Smith WJ, Xue GP, McSweeney CS. Expression of a modified Neocallimastix patriciarum xylanase in Butyrivibrio fibrisolvens digests more fibre but cannot effectively compete with highly fibrolytic bacteria in the rumen. J Appl Microbiol 2001; 90:388-96. [PMID: 11298234 DOI: 10.1046/j.1365-2672.2001.01257.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS This study investigated the competitive abilities of two Neocallimastix patriciarum-derived xylanases constructs in Butyrivibrio fibrisolvens H17c (xynA and pUMSX) and their ability to compete in vivo. METHODS AND RESULTS The digestibility of neutral detergent fibre (NDF) increased during co-culture of xynA or pUMSX and weakly cellulolytic, but not with highly cellulolytic, ruminococci. Competition studies among xynA, pUMSX and cellulolytic consortia demonstrated that xynA was the fittest. XynA did not persist at high levels in the rumen and was undetectable after 22 days. CONCLUSION The construction of recombinant xylanolytic B. fibrisolvens does improve the digestibility of fibre above that of the native, but digestibility is still less than that of the most potent fibre digesters such as ruminococci. SIGNIFICANCE AND IMPACT OF THE STUDY Fibre digestion may be improved by genetic manipulation of ruminal bacteria but ecological parameters, such as persistence in vivo and the niche of the organism, must be taken into account.
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Affiliation(s)
- D O Krause
- CSIRO Livestock Industries, Long Pocket Laboratories, Indooroopilly, Queensland, Australia.
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37
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Wang Y, McAllister TA, Rode LM, Beauchemin KA, Morgavi DP, Nsereko VL, Iwaasa AD, Yang W. Effects of an exogenous enzyme preparation on microbial protein synthesis, enzyme activity and attachment to feed in the Rumen Simulation Technique (Rusitec). Br J Nutr 2001; 85:325-32. [PMID: 11299078 DOI: 10.1079/bjn2000277] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The effects of an exogenous enzyme preparation, the application method and feed type on ruminal fermentation and microbial protein synthesis were investigated using the rumen simulation technique (Rusitec). Steam-rolled barley grain and chopped alfalfa hay were sprayed with water (control, C), an enzyme preparation with a predominant xylanase activity (EF), or autoclaved enzyme (AEF) 24 h prior to feeding, or the enzyme was supplied in the buffer infused into the Rusitec (EI). Microbial N incorporation was measured using (15NH4)2SO4 in the buffer. Spent feed bags were pummelled mechanically in buffer to segregate the feed particle-associated (FPA) and feed particle-bound (FPB) bacterial fractions. Enzymes applied to feed reduced neutral-detergent fibre content, and increased the concentration of reducing sugars in barley grain, but not alfalfa hay. Ruminal cellulolytic bacteria were more numerous with EF than with C. Disappearance of DM from barley grain was higher with EF than with C, but alfalfa was unaffected by EF. Treatment EF increased incorporation of 15N into FPA and FPB fractions at 24 and 48 h. In contrast, AEF reduced the 24 h values, relative to C; AEF and C were similar at 48 h. Infused enzyme (EI) did not affect 15N incorporation. Xylanase activity in effluent was increased by EF and EI, compared to C, but not by AEF. Xylanase activity in FPA was higher at 48 h than at 24 h with all treatments; it was higher with EF than C at 24 and 48 h, but was not altered by AEF or EI. Applying enzymes onto feeds before feeding was more effective than dosing directly into the artificial rumen for increasing ruminal fibrolytic activity.
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Affiliation(s)
- Y Wang
- Agriculture and Agri-Food Canada Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1
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Whitford MF, McPherson MA, Forster RJ, Teather RM. Identification of bacteriocin-like inhibitors from rumen Streptococcus spp. and isolation and characterization of bovicin 255. Appl Environ Microbiol 2001; 67:569-74. [PMID: 11157218 PMCID: PMC92622 DOI: 10.1128/aem.67.2.569-574.2001] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococci obtained from rumen sources were tested for the production of antibacterial compounds using a deferred-antagonism plating assay. Of 35 isolates tested, 7 were identified that inhibited the growth of other streptococci. None of the inhibitory activity was due to bacteriophage. Three isolates, LRC0253, LRC0255, and LRC0476, were selected for further characterization. Analysis of 16S ribosomal DNA indicated that LRC0476 was a strain of Streptococcus bovis, while isolates LRC0253 and LRC0255 are likely strains of Streptococcus gallolyticus. The antibacterial compounds produced by these bacteria were protease sensitive, remained active in a pH range from 1 to 12, and did not lose activity after heating at 100 degrees C for 15 min. The inhibitory peptide from strain LRC0255 was purified using pH-dependent adsorption and desorption to bacterial cells, followed by ammonium sulfate precipitation and reversed-phase chromatography and gel filtration. The peptide was 6 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. An oligonucleotide probe based on the N-terminal sequence of the purified peptide was used to identify the gene encoding the inhibitory peptide. The antibacterial peptide has characteristics that are very similar to those described for class II bacteriocins of gram-positive bacteria.
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Affiliation(s)
- M F Whitford
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada T1J 4B1
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Chen J, Weimer P. Competition among three predominant ruminal cellulolytic bacteria in the absence or presence of non-cellulolytic bacteria. MICROBIOLOGY (READING, ENGLAND) 2001; 147:21-30. [PMID: 11160797 DOI: 10.1099/00221287-147-1-21] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Competition among three species of ruminal cellulolytic bacteria - Fibrobacter succinogenes S85, Ruminococcus flavefaciens FD-1 and Ruminococcus albus 7 - was studied in the presence or absence of the non-cellulolytic ruminal bacteria Selenomonas ruminantium or Streptococcus bovis. Co-cultures were grown under either batch or continuous conditions and populations were estimated using species-specific oligonucleotide probes to 16S rRNA. The three cellulolytic species co-existed in cellobiose batch co-culture, but inclusion of either Sel. ruminantium or Str. bovis yielded nearly a monoculture of the non-cellulolytic competitor. In cellobiose chemostats, R. albus completely dominated the triculture, but R. flavefaciens became predominant over F. succinogenes and R. albus when Sel. ruminantium was co-inoculated into the chemostats. Similar effects on competition were observed in the presence of Str. bovis at a lower (0.021 h(-1)), but not at a higher (0.045 h(-1)) dilution rate. In cellulose batch co-cultures, R. albus was more abundant than both F. succinogenes and R. flavefaciens, regardless of the presence of the non-cellulolytic species. Co-existence among the three cellulolytic species was observed in almost all cellulose chemostats, but Sel. ruminantium altered the relative proportions of the cellulolytic species. R. albus and R. flavefaciens were found to produce inhibitors that suppressed growth of R. flavefaciens and F. succinogenes, respectively. These data indicate that interactions among cellulolytic bacteria, while complex, can be modified further by non-cellulolytic species.
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Affiliation(s)
- J Chen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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40
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Kageyama A, Sakamoto M, Benno Y. Rapid identification and quantification of Collinsella aerofaciens using PCR. FEMS Microbiol Lett 2000; 183:43-7. [PMID: 10650200 DOI: 10.1111/j.1574-6968.2000.tb08931.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The number and incidence of Collinsella aerofaciens in the human intestine are the highest among Gram-positive non-spore-forming bacilli. Identification of this species is very difficult and requires considerable time. A PCR-based identification system using C. aerofaciens-specific primers is described. Using this PCR method, we identified 181 C. aerofaciens-like species isolated from human feces. These 181 strains were identified using the traditional method in past studies. Results of both methods matched. The direct detection method was performed using human feces samples from seven adults. Nested PCR was applied directly to the samples and all seven samples were positive. Quantification studies were performed using LightCycler¿trade mark omitted¿. The assay uses a double-stranded DNA dye to continuously monitor product formation and in a short time is able to quantify samples to 5 log units in concentration.
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Affiliation(s)
- A Kageyama
- Japan Collection of Microorganisms, The Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama, Japan.
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41
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Brookman JL, Mennim G, Trinci APJ, Theodorou MK, Tuckwell DS. Identification and characterization of anaerobic gut fungi using molecular methodologies based on ribosomal ITS1 and 185 rRNA. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 2):393-403. [PMID: 10708378 DOI: 10.1099/00221287-146-2-393] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gut fungi are an unusual group of zoosporic fungi occupying a unique ecological niche, the anaerobic environment of the rumen. They exhibit two basic forms, with nuclear migration throughout the hyphal mass for polycentric species and with concentration of nuclear material in a zoosporangium for monocentric species. Differentiation between isolates of these fungi is difficult using conventional techniques. In this study, DNA-based methodologies were used to examine the relationships within and between two genera of monocentric gut fungi gathered from various geographical locations and host animals. The ribosomal ITS1 sequence from 16 mono- and 4 polycentric isolates was PCR-amplified and sequenced; the sequences obtained were aligned with published sequences and phylogenetic analyses were performed. These analyses clearly differentiate between the two genera and reflect the previously published physiological conclusions that Neocallimastix spp. constitute a more closely related genus than the relatively divergent genus Piromyces. The analyses place two type species N. frontalis and N. hurleyensis together but, contrary to a recent suggestion in the literature, place them apart from the other agreed species N. patriciarum. In situ hybridization and slot-blotting were investigated as potential methods for detection of and differentiation between monocentric gut fungi. DNA slot-blot analysis using ribosomal sequences is able to differentiate between gut fungal genera and thus has considerable potential for use in ecological studies of these organisms.
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Affiliation(s)
- J L Brookman
- Institute of Grasslands and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK2
- School of Biological Sciences, 2.205 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK1
| | - G Mennim
- Institute of Grasslands and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK2
- School of Biological Sciences, 2.205 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK1
| | - A P J Trinci
- School of Biological Sciences, 2.205 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK1
| | - M K Theodorou
- Institute of Grasslands and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK2
| | - D S Tuckwell
- School of Biological Sciences, 2.205 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK1
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42
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McSweeney C, Dalrymple B, Gobius K, Kennedy P, Krause D, Mackie R, Xue G. The application of rumen biotechnology to improve the nutritive value of fibrous feedstuffs: pre- and post-ingestion. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0301-6226(99)00032-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ricke SC, Pillai SD. Conventional and molecular methods for understanding probiotic bacteria functionality in gastrointestinal tracts. Crit Rev Microbiol 1999; 25:19-38. [PMID: 10342098 DOI: 10.1080/10408419991299176] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The recent successes of probiotic application to limit colonization of foodborne pathogens in the gastrointestinal tracts of food animals ensures continued commercialization and widespread use of such cultures. Given that the the fermentation response and ecological balance of the probiotic consortium appears to be essential for the effectiveness of the cultures, it is essential to develop a methodology to accurately identify and quantitate these organisms during commercial production as well as successful in vivo colonization after administration. However, if further optimization of the effectiveness of defined cultures is to be achieved, methods to assess expression of key metabolic processes occurring during establishment of the probiotic culture as well as its subsequent ability to limit foodborne pathogen colonization are needed. Conventional methods to study individual probiotic gastrointestinal organisms include selective plating to identify specific nutritional groups, but the requirement of strict anaerobiosis for the obligate anaerobic members of these cultures can confound sample handling and preparation. Immunological methods can circumvent some of these problems but are somewhat limited for assessing functionality. The main advantage of using molecular tools is that the genetic diversity of the microflora, as well as their gene activity data are obtainable, both at the community level and at the single species level. Methods are currently available that permit studying individual members of microbial consortia, fluxes in community diversity, spatial distribution of consortia members, and the expression of specific microbial genes within communities. These methods involve the utilization of both DNA- and RNA-targeted probes, gene amplification protocols, and mRNA analysis. The study of mechanisms and functionality can only enhance the potential of probiotic cultures for limiting foodborne pathogen colonization.
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Affiliation(s)
- S C Ricke
- Poultry Science Department, Texas A&M University, College Station 77843-2472, USA
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Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 1999; 69:1035S-1045S. [PMID: 10232646 DOI: 10.1093/ajcn/69.5.1035s] [Citation(s) in RCA: 781] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The gastrointestinal tract of a normal fetus is sterile. During the birth process and rapidly thereafter, microbes from the mother and surrounding environment colonize the gastrointestinal tract of the infant until a dense, complex microbiota develops. The succession of microbes colonizing the intestinal tract is most marked in early development, during which the feeding mode shifts from breast-feeding to formula feeding to weaning to the introduction of solid food. Dynamic balances exist between the gastrointestinal microbiota, host physiology, and diet that directly influence the initial acquisition, developmental succession, and eventual stability of the gut ecosystem. In this review, the development of the intestinal microbiota is discussed in terms of initial acquisition and subsequent succession of bacteria in human infants. Intrinsic and extrinsic factors influencing succession and their health significance are discussed. The advantages of modern molecular ecology techniques that provide sensitive and specific, culture-independent evaluation of the gastrointestinal ecosystem are introduced and discussed briefly. Further advances in our understanding of developmental microbial ecology in the neonatal gastrointestinal tract are dependent on the application of these modern molecular techniques.
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Affiliation(s)
- R I Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana 61801, USA.
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45
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Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA. Appl Environ Microbiol 1999; 65:1516-23. [PMID: 10103245 PMCID: PMC91215 DOI: 10.1128/aem.65.4.1516-1523.1999] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The feasibility of using probes directed towards ribosomal DNAs (rDNAs) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. Hybridizations were performed with membrane-bound nucleic acids by using seven group-specific DNA oligonucleotide probes complementary to 16S rRNA coding regions. These included a general eubacterial probe and probes encompassing most members of the gram-negative, mesophilic sulfate-reducing bacteria (SRB). DNA was extracted from sediment samples, and contaminating materials were removed by a series of steps. Efficiency of DNA extraction was 48% based on the recovery of tritiated plasmid DNA added to samples prior to extraction. Reproducibility of the extraction procedure was demonstrated by hybridizations to replicate samples. Numbers of target cells in samples were estimated by comparing the amount of hybridization to extracted DNA obtained with each probe to that obtained with a standard curve of genomic DNA for reference strains included on the same membrane. In June, numbers of SRB detected with an SRB-specific probe ranged from 6.0 x 10(7) to 2.5 x 10(9) (average, 1.1 x 10(9) +/- 5.2 x 10(8)) cells g of sediment-1. In September, numbers of SRB detected ranged from 5.4 x 10(8) to 7.3 x 10(9) (average, 2.5 x 10(9) +/- 1.5 x 10(9)) cells g of sediment-1. The capability of using rDNA probes to estimate cell numbers by hybridization to DNA extracted from complex matrices permits initiation of detailed studies on community composition and changes in communities based on cell numbers in formerly intractable environments.
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46
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Chan W, Dehority B. Production of Ruminococcus flavefaciens growth inhibitor(s) by Ruminococcus albus. Anim Feed Sci Technol 1999. [DOI: 10.1016/s0377-8401(98)00234-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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47
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Weimer PJ, Waghorn GC, Odt CL, Mertens DR. Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J Dairy Sci 1999; 82:122-34. [PMID: 10022014 DOI: 10.3168/jds.s0022-0302(99)75216-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The effects of four contrasting diets were determined on populations of three species of ruminal cellulolytic bacteria (Ruminococcus albus, Ruminococcus flavefaciens, and Fibrobacter succinogenes) using oligonucleotide probes to rRNA. Diets based on alfalfa silage or corn silage as the primary fiber source were formulated to contain either 24 or 32% neutral detergent fiber measured after alpha-amylase treatment. The diets were fed twice daily to four ruminally fistulated, lactating Holstein cows in a trial using a Latin square design. The cows fed the alfalfa silage diets had higher dry matter intakes and milk production and smaller pH fluctuations than did cows fed the corn silage diets (0.3 vs. 0.8 units). The total populations of the three cellulolytic species at 3 h after feeding ranged from 0.3 to 3.9% of the bacterial domain; R. albus was generally the most abundant of the three species. The data are in general agreement with population assessments obtained by some traditional methods of culture enumeration. Although diet and individual cows had major effects on ruminal pH and volatile fatty acid concentrations and on milk production and composition, differences in cellulolytic populations that were attributable to individual cows were larger than those attributable to diet, suggesting that each cow maintained a unique assemblage of cellulolytic species.
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Affiliation(s)
- P J Weimer
- US Dairy Forage Research Center, USDA-ABS, University of Wisconsin, Madison 53706, USA
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48
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Morovský M, Pristas P, Czikková S, Javorský P. A bacteriocin-mediated antagonism by Enterococcus faecium BC25 against ruminal Streptococcus bovis. Microbiol Res 1998; 153:277-81. [PMID: 9880931 DOI: 10.1016/s0944-5013(98)80012-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A bacteriocin-like activity produced by Enterococcus faecium BC25, isolated from the the rumen of a cow, was partially purified and characterized. The active substance was prepared by ammonium sulfate and chloroform/methanol precipitation of culture supernatant. The bacteriocin was a protein of molecular mass 17.5 kDa. Activity was inactivated by trypsin and proteinase K. The bacteriocin BC25 inhibited growth of amylolytic ruminal strains of Streptococcus bovis, including S. bovis AO 24/85. Results showed that bacteriocine substance BC25 has a bacteriostatic effect when present in concentrations exceeding 125 AU/ml. Agar overlays and batch culture growth experiments proved that E. faecium BC25 was producing bacteriocin that inhibited the growth of S. bovis.
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Affiliation(s)
- M Morovský
- Department of Biochemistry, Faculty of Sciences, P.J. Safárik University, Kosice, Slovakia
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Reilly K, Attwood GT. Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl Environ Microbiol 1998; 64:907-13. [PMID: 9501430 PMCID: PMC106345 DOI: 10.1128/aem.64.3.907-913.1998] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A competitive PCR technique was used to enumerate the proteolytic bacterium Clostridium proteoclasticum from the rumen. A PCR primer, which circumscribes this organism and several closely related strains, was designed for a variable region within their 16S rRNA genes and was used in conjunction with a universal forward primer. This primer pair was tested for specificity against 85 ruminal bacterial strains. An internal control DNA was constructed for use in competitive PCRs and was shown to amplify under the same reaction conditions and with the same amplification efficiency as the target DNA. DNA from a known number of C. proteoclasticum cells was coamplified with the internal control to construct a standard curve. Rumen samples were collected from eight dairy cows fed four diets in rotation: high nitrogen, high nitrogen supplemented with carbohydrate, low nitrogen, and low nitrogen supplemented with carbohydrate. DNA extracted from these and spiked with internal control DNA was amplified with the C. proteoclasticum primer pair. The relative intensities of the PCR products were used to quantitate the numbers of C. proteoclasticum cell equivalents from the rumen samples. The numbers ranged from 2.01 x 10(6) ml-1 to 3.12 x 10(7) ml-1. There was no significant effect on the numbers of C. proteoclasticum detected in rumen samples among cows fed the four diets. The utility of the competitive PCR approach for quantifying ruminal bacterial populations in vivo and the occurrence of C. proteoclasticum in forage-fed dairy cows are discussed.
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Affiliation(s)
- K Reilly
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
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Abstract
The rumen of sheep and cattle represents a mobile, self-sustaining fermentation system for plant material. Analysis of the rumen flora continues to provide fundamental knowledge of anaerobic microbiology and is now yielding microbial genes that have potential in biotechnology. Recent research has provided fascinating glimpses into the microbial enzyme systems that degrade plant material and into the complex interplay among members of the rumen community.
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Affiliation(s)
- H J Flint
- Rowett Research Institute, Aberdeen, UK.
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