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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Huaiquipán R, Quiñones J, Díaz R, Velásquez C, Sepúlveda G, Velázquez L, Paz EA, Tapia D, Cancino D, Sepúlveda N. Review: Effect of Experimental Diets on the Microbiome of Productive Animals. Microorganisms 2023; 11:2219. [PMID: 37764062 PMCID: PMC10536378 DOI: 10.3390/microorganisms11092219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023] Open
Abstract
The microorganisms that inhabit the gastrointestinal tract are responsible for multiple chains of reactions that affect their environment and modify the internal metabolism, their study receives the name of microbiome, which has become more relevant in recent years. In the near future, the challenges related to feeding are anticipated to escalate, encompassing the nutritional needs to sustain an overpopulated world. Therefore, it is expected that a better understanding of the interactions between microorganisms within the digestive tract will allow their modulation in order to provide an improvement in the immune system, feed efficiency or the promotion of nutritional characteristics in production animals, among others. In the present study, the main effects of experimental diets in production animals were described, emphasizing the diversity of the bacterial populations found in response to the diets, ordering them between polygastric and monogastric animals, and then describing the experimental diets used and their effect on the microorganisms. It is hoped that this study will help as a first general approach to the study of the role of the microbiome in production animals under different diets.
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Affiliation(s)
- Rodrigo Huaiquipán
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - John Quiñones
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Rommy Díaz
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Carla Velásquez
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Gastón Sepúlveda
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Lidiana Velázquez
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Erwin A. Paz
- UWA Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - Daniela Tapia
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - David Cancino
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Néstor Sepúlveda
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
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3
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Frolova M, Yudin S, Makarov V, Glazunova O, Alikina O, Markelova N, Kolzhetsov N, Dzhelyadin T, Shcherbakova V, Trubitsyn V, Panyukov V, Zaitsev A, Kiselev S, Shavkunov K, Ozoline O. Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity. Life (Basel) 2021; 11:life11111246. [PMID: 34833122 PMCID: PMC8620312 DOI: 10.3390/life11111246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 02/07/2023] Open
Abstract
Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this "rare" strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.
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Affiliation(s)
- Maria Frolova
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Sergey Yudin
- Centre for Strategic Planning of Federal Medical-Biological Agency of Russia, 119121 Moscow, Russia; (S.Y.); (V.M.)
| | - Valentin Makarov
- Centre for Strategic Planning of Federal Medical-Biological Agency of Russia, 119121 Moscow, Russia; (S.Y.); (V.M.)
| | - Olga Glazunova
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Olga Alikina
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Natalia Markelova
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Nikolay Kolzhetsov
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Timur Dzhelyadin
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, 142290 Pushchino, Russia; (V.S.); (V.T.)
| | - Vladimir Trubitsyn
- Laboratory of Anaerobic Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, 142290 Pushchino, Russia; (V.S.); (V.T.)
| | - Valery Panyukov
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Alexandr Zaitsev
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Sergey Kiselev
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
- Correspondence: (K.S.); (O.O.)
| | - Olga Ozoline
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
- Correspondence: (K.S.); (O.O.)
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4
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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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Monteiro HF, Faciola AP. Ruminal acidosis, bacterial changes, and lipopolysaccharides. J Anim Sci 2020; 98:5881933. [PMID: 32761212 DOI: 10.1093/jas/skaa248] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
Acute and subacute ruminal acidosis (SARA) are common nutritional problems in both beef and dairy cattle. Therefore, the objective of this review is to describe how ruminal Gram-negative bacteria could contribute to the pathogenesis of ruminal acidoses, by releasing lipopolysaccharides (LPS; a component of their cell wall) in the ruminal fluid. When cattle consume excessive amounts of highly fermentable carbohydrates without prior adaptation, normal fermentation become disrupted. The fermentation of these carbohydrates quickly decreases ruminal pH due to the accumulation of short-chain fatty acids and lactate in the rumen. As a consequence, ruminal epithelium may be damaged and tissue function could be impaired, leading to a possible translocation of pathogenic substances from the rumen into the bloodstream. Such changes in fermentation are followed by an increase in Gram-positive bacteria while Gram-negative bacteria decrease. The lyses of Gram-negative bacteria during ruminal acidosis increase LPS concentration in the ruminal fluid. Because LPS is a highly proinflammatory endotoxin in the circulatory system, past studies have raised concerns regarding ruminal LPS contribution to the pathogenesis of ruminal acidosis. Although animals that undergo these disorders do not always have an immune response, recent studies showed that different Gram-negative bacteria have different LPS composition and toxicity, which may explain the differences in immune response. Given the diversity of Gram-negative bacteria in the rumen, evaluating the changes in the bacterial community during ruminal acidosis could be used as a way to identify which Gram-negative bacteria are associated with LPS release in the rumen. By identifying and targeting ruminal bacteria with possible pathogenic LPS, nutritional strategies could be created to overcome, or at least minimize, ruminal acidosis.
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Affiliation(s)
- Hugo F Monteiro
- Department of Animal Sciences, University of Florida, Gainesville, FL
| | - Antonio P Faciola
- Department of Animal Sciences, University of Florida, Gainesville, FL
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Moraïs S, Mizrahi I. Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem. FEMS Microbiol Rev 2019; 43:362-379. [PMID: 31050730 PMCID: PMC6606855 DOI: 10.1093/femsre/fuz007] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/05/2019] [Indexed: 12/20/2022] Open
Abstract
The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.
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Affiliation(s)
- Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
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7
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Kameshwar AKS, Qin W. Genome Wide Analysis Reveals the Extrinsic Cellulolytic and Biohydrogen Generating Abilities of Neocallimastigomycota Fungi. J Genomics 2018; 6:74-87. [PMID: 29928466 PMCID: PMC6004548 DOI: 10.7150/jgen.25648] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/25/2018] [Indexed: 11/26/2022] Open
Abstract
Ruminating animals, especially cattle lack the carbohydrate active enzyme encoding genes which are required for the degradation of the glycosidic linkages of plant cell wall carbohydrates (such as cellulose, hemicellulose, lignin and pectin). Thus, ruminating animals are completely dependent on the microorganisms (anaerobic bacteria and fungi, methanogenic archaea and protozoa) residing in their rumen (hindgut). In this study, we have retrieved and analyzed the complete genome wide annotations of the Neocallimastigomycota division fungi such as Anaeromyces robustus, Neocallismatix californiae, Orpinomyces sp, Piromyces finnis, Piromyces sp E2. We have retrieved the InterPro, CAZy, KOG, KEGG, SM Clusters and MEROPS genome level data of these anaerobic fungi from JGI-MycoCosm database. Results obtained in our study reveals that, the genomes of anaerobic fungi completely lack genes encoding for lignin degrading auxiliary activity enzymes. Contrastingly, these fungi outnumbered other fungi by having highest number of CAZyme encoding genes. The genes encoding for dockerins and carbohydrate binding modules exaggerated other CAZymes which are involved in the structure and functioning of cellulosomes. Presence of cellulosomes and higher number of carbohydrate transport and metabolism genes also endorses the plant cell wall carbohydrate degrading abilities of these fungi. We also reported the tentative total cellulolytic, hemicellulolytic and pectinolytic abilities. And we have explicitly reported the genes, enzymes and the mechanisms involved in structure and functioning of the cellulosomes and hydrogenosomes. Our present work reveals the genomic machinery underlying the extrinsic plant cell wall degrading abilities of the anaerobic fungi. Results obtained in our study can be significantly applied in improving the gut health of cattle and especially in the fields of biofuel, biorefining and bioremediation-based industries.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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8
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Perea K, Perz K, Olivo SK, Williams A, Lachman M, Ishaq SL, Thomson J, Yeoman CJ. Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small-intestine-located microbiota. J Anim Sci 2017; 95:2585-2592. [PMID: 28727071 DOI: 10.2527/jas.2016.1222] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several studies have revealed differences in rumen-located microbes between greatly efficient and inefficient animals; however, how the microbiota vary in the hind gastrointestinal tract (GIT) has only been sparsely explored and how they vary in the small intestine remains to be determined. We therefore sampled the microbiota of the duodenum, jejunum, ileum, colon, and colorectally-obtained feces, in addition to the rumen of 12 lambs that, in a residual feed intake trial, were found to be at either extreme of feed efficiency phenotypes. The 16S rRNA gene (V3-V4 region) profiles of all samples were analyzed and revealed unique microbiota in all GIT locations except the jejunum and ileum (ANOSIM > 0.2, < 0.001). Measures of β-diversity revealed greater dissimilarity between more anatomically distant GIT locations (e.g., Rumen-Duodenum, ANOSIM = 0.365, < 0.001; Rumen-Colon, ANOSIM = 1, < 0.001) with the nearest distal region typically more similar than the nearest proximal location. The relative abundances of 13 operational taxonomic units (OTUs) from the duodenum, jejunum, colon, and feces, as well as the rumen, differed between efficient and inefficient animals (Bonferroni corrected, < 0.05), while another 2 OTUs trended toward significance. These OTUs were classified as taxa with known roles in fibrolysis (Fibrobacteres, Ruminococcaceae, and Saccharofermentans) and others that are commonly associated with health (Bifidobacteriaceae, and Christensenellaceae) and dysbiosis (Proteobacteria). Our findings show biospatial delineations of microbiota throughout the GIT and suggest that feed efficiency extends beyond the rumen, transcending these regions, and involves increases in both rumen- and colon-located fibrolytic taxa, increases in bifidobacterial species in the small intestine, and reductions in small intestine and distal GIT-located Proteobacteria.
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Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 2017; 7:42355. [PMID: 28186207 PMCID: PMC5301203 DOI: 10.1038/srep42355] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/08/2017] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrading Ruminococcus flavefaciens FD-1 genome revealed a particularly elaborate cellulosome system. In total, 223 dockerin-bearing ORFs potentially involved in cellulosome assembly and a variety of multi-modular scaffoldins were identified, and the dockerins were classified into six major groups. Here, extensive screening employing three complementary medium- to high-throughput platforms was used to characterize the different cohesin-dockerin specificities. The platforms included (i) cellulose-coated microarray assay, (ii) enzyme-linked immunosorbent assay (ELISA) and (iii) in-vivo co-expression and screening in Escherichia coli. The data revealed a collection of unique cohesin-dockerin interactions and support the functional relevance of dockerin classification into groups. In contrast to observations reported previously, a dual-binding mode is involved in cellulosome cell-surface attachment, whereas single-binding interactions operate for cellulosome integration of enzymes. This sui generis cellulosome model enhances our understanding of the mechanisms governing the remarkable ability of R. flavefaciens to degrade carbohydrates in the bovine rumen and provides a basis for constructing efficient nano-machines applied to biological processes.
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Affiliation(s)
- Vered Israeli-Ruimy
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Pedro Bule
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Yoav Barak
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Michal Slutzki
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Hamberg
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Vânia Cardoso
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Victor D. Alves
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Bryan A. White
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Harry J. Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, Scotland, UK
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Carlos M. G. A. Fontes
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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Abstract
There are a range of methodologies available to study the human microbiota, ranging from traditional approaches such as culturing through to state-of-the-art developments in next generation DNA sequencing technologies. The advent of molecular techniques in particular has opened up tremendous new avenues for research, and has galvanised interest in the study of our microbial inhabitants. Given the dazzling array of available options, however, it is important to understand the inherent advantages and limitations of each technique so that the best approach can be employed to address the particular research objective. In this chapter we cover some of the most widely used current techniques in human microbiota research and highlight the particular strengths and caveats associated with each approach.
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Affiliation(s)
- Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters. Appl Environ Microbiol 2015; 82:1519-1529. [PMID: 26712547 DOI: 10.1128/aem.03360-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/18/2015] [Indexed: 01/03/2023] Open
Abstract
Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions.
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Toumi J, Miladi B, Farhat A, Nouira S, Hamdi M, Gtari M, Bouallagui H. Microbial ecology overview during anaerobic codigestion of dairy wastewater and cattle manure and use in agriculture of obtained bio-fertilisers. BIORESOURCE TECHNOLOGY 2015; 198:141-149. [PMID: 26386416 DOI: 10.1016/j.biortech.2015.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/03/2015] [Accepted: 09/05/2015] [Indexed: 06/05/2023]
Abstract
The anaerobic co-digestion of dairy wastewater (DW) and cattle manure (CM) was examined and associated with microbial community's structures using Denaturing Gradient Gel Electrophoresis (DGGE). The highest volatile solids (VS) reduction yield of 88.6% and biogas production of 0.87 L/g VS removed were obtained for the C/N ratio of 24.7 at hydraulic retention time (HRT) of 20 days. The bacterial DGGE profile showed significant abundance of Uncultured Bacteroidetes, Firmicutes and Synergistetes bacterium. The Syntrophomonas strains were discovered in dependent association to H2-using bacteria such as Methanospirillum sp., Methanosphaera sp. and Methanobacterium formicicum. These syntrophic associations are essential in anaerobic digesters allow them to keep low hydrogen partial pressure. However, high concentrations of VFA produced from dairy wastes acidification allow the growth of Methanosarcina species. The application of the stabilised anaerobic effluent on the agriculture soil showed significant beneficial effects on the forage corn and tomato plants growth and crops.
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Affiliation(s)
- Jihen Toumi
- UR-Biodiversity and Biology of Populations, FST, University of Elmanar, Tunis, Tunisia; LR-Microbial Ecology and Technology, INSAT, University of Carthage, Tunis, Tunisia
| | - Baligh Miladi
- LR-Microbial Ecology and Technology, INSAT, University of Carthage, Tunis, Tunisia
| | - Amel Farhat
- LR-Microbial Ecology and Technology, INSAT, University of Carthage, Tunis, Tunisia
| | - Said Nouira
- UR-Biodiversity and Biology of Populations, FST, University of Elmanar, Tunis, Tunisia
| | - Moktar Hamdi
- LR-Microbial Ecology and Technology, INSAT, University of Carthage, Tunis, Tunisia
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar, Tunisia
| | - Hassib Bouallagui
- LR-Microbial Ecology and Technology, INSAT, University of Carthage, Tunis, Tunisia.
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13
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Rozman Grinberg I, Yin G, Borovok I, Berg Miller ME, Yeoman CJ, Dassa B, Yu Z, Mizrahi I, Flint HJ, Bayer EA, White BA, Lamed R. Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome. FEMS Microbiol Lett 2014; 362:1-10. [PMID: 25673657 DOI: 10.1093/femsle/fnu047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ruminococcus albus, a cellulolytic bacterium, is a critical member of the rumen community. Ruminococcus albus lacks a classical cellulosome complex, but it possesses a unique family 37 carbohydrate-binding module (CBM37), which is integrated into a variety of carbohydrate-active enzymes. We developed a potential molecular tool for functional phylotyping of the R. albus population in the rumen, based on a variable region in the cel48A gene. cel48A encodes a single copy of the CBM37-associated family 48 glycoside hydrolase in all known strains of this bacterium. A segment of the cel48A gene was amplified from rumen metagenomic samples of four bovines, and its abundance and diversity were evaluated. Analysis of the obtained sequences revealed the co-existence of multiple functional phylotypes of cel48A in all four animals. These included sequences identical or similar to those of R. albus isolates (reference strains), as well as several novel sequences. The dominant cel48A type varied among animals. This method can be used for detection of intraspecific diversity of R. albus in metagenomic samples. Together with scaC, a previously reported gene marker for R. flavefaciens, we present a set of two species-specific markers for phylotyping of Ruminococci in the herbivore rumen.
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Affiliation(s)
- Inna Rozman Grinberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Guohua Yin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | | | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zhongtang Yu
- The MAPLE Research Initiative, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Itzhak Mizrahi
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB21 9SB, UK
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bryan A White
- Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. PLoS One 2014; 9:e99221. [PMID: 24992679 PMCID: PMC4081043 DOI: 10.1371/journal.pone.0099221] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022] Open
Abstract
Background A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels. Methodology/Principal Findings Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37). Conclusions/Significance Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.
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15
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Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol 2014; 22:267-74. [PMID: 24698744 DOI: 10.1016/j.tim.2014.03.001] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 01/02/2023]
Abstract
The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.
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16
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Mikaelyan A, Strassert JFH, Tokuda G, Brune A. The fibre-associated cellulolytic bacterial community in the hindgut of wood-feeding higher termites (Nasutitermesspp.). Environ Microbiol 2014. [DOI: 10.1111/1462-2920.12425] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Jürgen F. H. Strassert
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Gaku Tokuda
- Tropical Biosphere Research Center; COMB; University of the Ryukyus; Nishihara Okinawa Japan
| | - Andreas Brune
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
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17
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Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome. PLoS One 2013; 8:e84033. [PMID: 24391873 PMCID: PMC3877134 DOI: 10.1371/journal.pone.0084033] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/11/2013] [Indexed: 12/14/2022] Open
Abstract
Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.
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18
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Abstract
The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana 59717-2900;
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19
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Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Appl Microbiol Biotechnol 2013; 98:2321-34. [PMID: 23989973 DOI: 10.1007/s00253-013-5144-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m(3) digester produced biogas with 57% methane, and chemical oxygen demand removal of 54%. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93% of the clones and 76% of the pyrotags. Of the Firmicutes, class Clostridia (52% pyrotags) was most abundant followed by class Bacilli (13% pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97% minimum similarity level. Fifteen OTUs were dominant (≥2% abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5% abundance), 75% were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99% of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.
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20
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Salama-Alber O, Jobby MK, Chitayat S, Smith SP, White BA, Shimon LJW, Lamed R, Frolow F, Bayer EA. Atypical cohesin-dockerin complex responsible for cell surface attachment of cellulosomal components: binding fidelity, promiscuity, and structural buttresses. J Biol Chem 2013; 288:16827-16838. [PMID: 23580648 PMCID: PMC3675615 DOI: 10.1074/jbc.m113.466672] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/07/2013] [Indexed: 01/01/2023] Open
Abstract
The rumen bacterium Ruminococcus flavefaciens produces a highly organized multienzyme cellulosome complex that plays a key role in the degradation of plant cell wall polysaccharides, notably cellulose. The R. flavefaciens cellulosomal system is anchored to the bacterial cell wall through a relatively small ScaE scaffoldin subunit, which bears a single type IIIe cohesin responsible for the attachment of two major dockerin-containing scaffoldin proteins, ScaB and the cellulose-binding protein CttA. Although ScaB recruits the catalytic machinery onto the complex, CttA mediates attachment of the bacterial substrate via its two putative carbohydrate-binding modules. In an effort to understand the structural basis for assembly and cell surface attachment of the cellulosome in R. flavefaciens, we determined the crystal structure of the high affinity complex (Kd = 20.83 nM) between the cohesin module of ScaE (CohE) and its cognate X-dockerin (XDoc) modular dyad from CttA at 1.97-Å resolution. The structure reveals an atypical calcium-binding loop containing a 13-residue insert. The results further pinpoint two charged specificity-related residues on the surface of the cohesin module that are responsible for specific versus promiscuous cross-strain binding of the dockerin module. In addition, a combined functional role for the three enigmatic dockerin inserts was established whereby these extraneous segments serve as structural buttresses that reinforce the stalklike conformation of the X-module, thus segregating its tethered complement of cellulosomal components from the cell surface. The novel structure of the RfCohE-XDoc complex sheds light on divergent dockerin structure and function and provides insight into the specificity features of the type IIIe cohesin-dockerin interaction.
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Affiliation(s)
| | - Maroor K Jobby
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Seth Chitayat
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Linda J W Shimon
- Chemical Services, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Ramat Aviv 69978, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Ramat Aviv 69978, Israel; Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
| | - Edward A Bayer
- Departments of Biological Chemistry, Rehovot 76100, Israel.
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Sukharnikov LO, Alahuhta M, Brunecky R, Upadhyay A, Himmel ME, Lunin VV, Zhulin IB. Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. J Biol Chem 2012; 287:41068-77. [PMID: 23055526 DOI: 10.1074/jbc.m112.405720] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Currently, the cost of cellulase enzymes remains a key economic impediment to commercialization of biofuels. Enzymes from glycoside hydrolase family 48 (GH48) are a critical component of numerous natural lignocellulose-degrading systems. Although computational mining of large genomic data sets is a promising new approach for identifying novel cellulolytic activities, current computational methods are unable to distinguish between cellulases and enzymes with different substrate specificities that belong to the same protein family. We show that by using a robust computational approach supported by experimental studies, cellulases and non-cellulases can be effectively identified within a given protein family. Phylogenetic analysis of GH48 showed non-monophyletic distribution, an indication of horizontal gene transfer. Enzymatic function of GH48 proteins coded by horizontally transferred genes was verified experimentally, which confirmed that these proteins are cellulases. Computational and structural studies of GH48 enzymes identified structural elements that define cellulases and can be used to computationally distinguish them from non-cellulases. We propose that the structural element that can be used for in silico discrimination between cellulases and non-cellulases belonging to GH48 is an ω-loop located on the surface of the molecule and characterized by highly conserved rare amino acids. These markers were used to screen metagenomics data for "true" cellulases.
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Affiliation(s)
- Leonid O Sukharnikov
- BioEnergy Science Center, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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22
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Sirohi SK, Singh N, Dagar SS, Puniya AK. Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 2012; 95:1135-54. [PMID: 22782251 DOI: 10.1007/s00253-012-4262-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/30/2022]
Abstract
Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.
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Affiliation(s)
- Sunil Kumar Sirohi
- Nutrition Biotechnology Laboratory, Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, 132001, Haryana, India.
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