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Sheridan PO, Odat MA, Scott KP. Establishing genetic manipulation for novel strains of human gut bacteria. Microbiome Res Rep 2023; 2:1. [PMID: 38059211 PMCID: PMC10696588 DOI: 10.20517/mrr.2022.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/29/2022] [Accepted: 12/12/2022] [Indexed: 12/08/2023]
Abstract
Recent years have seen the development of high-accuracy and high-throughput genetic manipulation techniques, which have greatly improved our understanding of genetically tractable microbes. However, challenges remain in establishing genetic manipulation techniques in novel organisms, owing largely to exogenous DNA defence mechanisms, lack of selectable markers, lack of efficient methods to introduce exogenous DNA and an inability of genetic vectors to replicate in their new host. In this review, we describe some of the techniques that are available for genetic manipulation of novel microorganisms. While many reviews exist that focus on the final step in genetic manipulation, the editing of recipient DNA, we particularly focus on the first step in this process, the transfer of exogenous DNA into a strain of interest. Examples illustrating the use of these techniques are provided for a selection of human gut bacteria in which genetic tractability has been established, such as Bifidobacterium, Bacteroides and Roseburia. Ultimately, this review aims to provide an information source for researchers interested in developing genetic manipulation techniques for novel bacterial strains, particularly those of the human gut microbiota.
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Affiliation(s)
- Paul O. Sheridan
- School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Ma’en Al Odat
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
| | - Karen P. Scott
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
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Mukhopadhya I, Martin JC, Shaw S, McKinley AJ, Gratz SW, Scott KP. Comparison of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers using next-generation sequencing and culturomics. Microbiome 2022; 10:171. [PMID: 36242064 PMCID: PMC9563177 DOI: 10.1186/s40168-022-01354-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Faecal samples are frequently used to characterise the gut microbiota in health and disease, yet there is considerable debate about how representative faecal bacterial profiles are of the overall gut community. A particular concern is whether bacterial populations associated with the gut mucosa are properly represented in faecal samples, since these communities are considered critical in the aetiology of gastrointestinal diseases. In this study we compared the profiles of the faecal and mucosal microbiota from ten healthy volunteers using bacterial culturing (culturomics) and next-generation sequencing targeting the 16S ribosomal nucleic acid (rRNA) gene. Paired fresh rectal biopsies and faecal samples were processed under stringent anaerobic conditions to maintain the viability of the bacteria. Four different sample types were analysed: faecal (F), faecal homogenised (FHg), biopsy tissue (B) and biopsy wash (BW) samples. RESULTS: There were no significant statistical differences in either bacterial richness or diversity between biopsy washes (BW) and faecal (F) or faecal homogenised (FHg) samples. Principal coordinates analysis of a Bray-Curtis distance matrix generated from sequence variant tables did not show distinct clustering between these samples (PERMANOVA; p = 0.972) but showed strong clustering of samples from individual donors. However, the rectal biopsy tissue (B) samples had a significantly altered bacterial signature with greater abundance of Proteobacteria and Acidobacteria compared to faecal (F) and faecal homogenised (FHg) samples. A total of 528 bacteria encompassing 92 distinct bacterial species were isolated and cultured from a subset of six volunteer samples (biopsy washes and faeces). This included isolation of 22 novel bacterial species. There was significant similarity between the bacterial species grown in anaerobic culture and those identified by 16S rRNA gene sequencing (Spearman correlation; rho = 0.548, p = 0.001). CONCLUSION This study showed that the bacterial profiles of paired faecal and rectal biopsy wash samples were very similar, validating the use of faecal samples as a convenient surrogate for rectal biopsy-associated microbiota. Anaerobic bacterial culture results showed similar taxonomic patterns to the amplicon sequence analysis disproving the dogma that culture-based methods do not reflect findings of molecular assessments of gut bacterial composition. Video abstract.
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Affiliation(s)
| | - Jennifer C. Martin
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Old Aberdeen, UK
- Current Address - All Wales Medical Genomics Service, Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Aileen J. McKinley
- Department of Surgery, Aberdeen Royal Infirmary Foresterhill, Aberdeen, UK
| | - Silvia W. Gratz
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Karen P. Scott
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
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Oyedemi OT, Shaw S, Martin JC, Ayeni FA, Scott KP. Changes in the gut microbiota of Nigerian infants within the first year of life. PLoS One 2022; 17:e0265123. [PMID: 35298505 PMCID: PMC8929609 DOI: 10.1371/journal.pone.0265123] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
The composition of the gut microbiota plays an important role in maintaining the balance between health and disease. However, there is considerably less information on the composition of the gut microbiota of non-Western communities. This study was designed to investigate the evolution in the gut microbiota in a cohort of Nigerian infants within the first year of life. Faecal samples were obtained monthly from 28 infants from birth for one year. The infants had been born by a mix of natural birth and caesarean section and were either breast-fed or mixed fed. Sequencing of the V1-V2 region of the 16S rRNA gene was used to characterise the microbiota. Short chain fatty acids and lactate present in each faecal sample were identified by gas chromatography. Microbial differences were observed between the vaginal and caesarean section delivered infants in samples collected within 7 days of life, although these differences were not observed in later samples. Exclusively breastfed infants had predominance of Ruminococcus gnavus, Collinsella, and Sutterella species. Different Bifidobacterium species dominated breast-fed compared to mixed fed infants. Clostridium, Enterococcus, Roseburia, and Coprococcus species were observed once the infants commenced weaning. Butyrate was first detected when weaning started between months 4–6 in the majority of the infants while total short chain fatty acid concentrations increased, and acetate and lactate remained high following the introduction of solid foods. The observed taxonomic differences in the gut microbiota between Nigerian infants, as well as butyrate production during weaning, were strongly influenced by diet, and not by birthing method. Introduction of local/solid foods encouraged the colonisation and evolution of specific marker organisms associated with carbohydrate metabolism.
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Affiliation(s)
- Omolanke T. Oyedemi
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Jennifer C. Martin
- The Rowett Institute, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Funmilola A. Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Department of Biology, Simmons University, Fenway, Boston, United States of America
- * E-mail: (KPS); (FAA)
| | - Karen P. Scott
- The Rowett Institute, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- * E-mail: (KPS); (FAA)
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Ventura M, van Sinderen D, Turroni F, Milani C, Munoz J, Haller D, Ross RP, Collado MC, Allen-Vercoe E, Del Rio D, Altermann E, Katayama T, Zoetendal EG, Belzer C, Mena P, Im SH, Gueimonde M, Margolles A, Ruiz L, Lacroix C, Stanton C, Barbara G, Saminen S, Scott KP, Barrangou R, Bottacini F, Marco ML. Editors' Prelude to Microbiome Research Reports. Microbiome Res Rep 2021; 1:1. [PMID: 38059066 PMCID: PMC10696583 DOI: 10.20517/mrr.2021.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/08/2023]
Affiliation(s)
- Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork Co. Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
| | - Jose Munoz
- Applied Sciences Department, Northumbria University, Newcastle Upon Tyne NE1 7RU, UK
| | - Dirk Haller
- Chair of Nutrition and Immunology, ZIEL - Institute for Food & Health, Freising, Technical University of Munich, Munich 80807, Germany
| | - R. Paul Ross
- APC Microbiome Ireland, University College, Cork Co. Cork, Ireland
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia 46007, Spain
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario P0R 1A0, Canada
| | - Daniele Del Rio
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
- Department of Food & Drugs, University of Parma, Parma 43126, Italy
| | - Eric Altermann
- AgResearch, Hopkirk Research Centre, Palmerston North 4410, New Zealand
- Riddet Institute, Massey University, Palmerston North 4410, New Zealand
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto 600-8586, Japan
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University, Wageningen 6700, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen 6700, The Netherlands
| | - Pedro Mena
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
- Department of Food & Drugs, University of Parma, Parma 43126, Italy
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 999007, South Korea
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry, Institute of Dairy Products of Asturias (IPLA-CSIC), Villaviciosa 33300, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry, Institute of Dairy Products of Asturias (IPLA-CSIC), Villaviciosa 33300, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry, Institute of Dairy Products of Asturias (IPLA-CSIC), Villaviciosa 33300, Spain
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zürich 8092, Switzerland
| | - Catherine Stanton
- Teagasc Moorepark Food Research Centre & APC Microbiome Ireland, Cork Co. Cork, Ireland
| | - Giovani Barbara
- Chair of Internal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40121, Italy
| | - Seppo Saminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku 20100, Finland
| | - Karen P. Scott
- Gut Health, Rowett Institute, University of Aberdeen, Aberdeen, Scotland AB53, UK
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh 25911, USA
| | - Francesca Bottacini
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork Co. Cork, Ireland
| | - Maria L. Marco
- Department of Food Science and Technology, University of California, Davis 95616, USA
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Smith NM, Maloney NG, Shaw S, Horgan GW, Fyfe C, Martin JC, Suter A, Scott KP, Johnstone AM. Daily Fermented Whey Consumption Alters the Fecal Short-Chain Fatty Acid Profile in Healthy Adults. Front Nutr 2020; 7:165. [PMID: 33102510 PMCID: PMC7556162 DOI: 10.3389/fnut.2020.00165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Gut microbiota influences many aspects of host health including immune, metabolic, and gut health. We examined the effect of a fermented whey concentrate (FWC) drink rich in L-(+)-Lactic acid, consumed daily, in 18 healthy men (n = 5) and women (n = 13) in free-living conditions. Objective: The aims of this 6-weeks pilot trial were to (i) identify changes in the gut microbiota composition and fecal short chain fatty acid (SCFA) profile, and (ii) to monitor changes in glucose homeostasis. Results: Total fecal SCFA (mM) concentration remained constant throughout the intervention. Proportionally, there was a significant change in the composition of different SCFAs compared to baseline. Acetate levels were significantly reduced (−6.5%; p < 0.01), coupled to a significant increase in the relative amounts of propionate (+2.2%; p < 0.01) and butyrate (+4.2%; p < 0.01), respectively. No changes in the relative abundance of any specific bacteria were detected. No significant changes were observed in glucose homeostasis in response to an oral glucose tolerance test. Conclusion: Daily consumption of a fermented whey product led to significant changes in fecal SCFA metabolite profile, indicating some potential prebiotic activity. These changes did not result in any detectable differences in microbiota composition. Post-hoc analysis indicated that baseline microbiota composition might be indicative of participants likely to see changes in SCFA levels. However, due to the lack of a control group these findings would need to be verified in a rigorously controlled trial. Future work is also required to identify the biological mechanisms underlying the observed changes in microbiota activity and to explore if these processes can be harnessed to favorably impact host health. Clinical Trial Registration: www.clinicaltrials.gov, identifier NCT03615339; retrospectively registered on 03/08/2018.
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Affiliation(s)
- Nicola M Smith
- School of Medicine, Medical Sciences and Nutrition, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Niamh G Maloney
- School of Medicine, Medical Sciences and Nutrition, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, United Kingdom
| | - Graham W Horgan
- Biomathematics & Statistics Scotland, University of Aberdeen, Aberdeen, United Kingdom
| | - Claire Fyfe
- School of Medicine, Medical Sciences and Nutrition, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Jennifer C Martin
- School of Medicine, Medical Sciences and Nutrition, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Karen P Scott
- School of Medicine, Medical Sciences and Nutrition, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Alexandra M Johnstone
- School of Medicine, Medical Sciences and Nutrition, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
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Sheridan PO, Martin JC, Scott KP. Conjugation Protocol Optimised for Roseburia inulinivorans and Eubacterium rectale. Bio Protoc 2020; 10:e3575. [PMID: 33659545 DOI: 10.21769/bioprotoc.3575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/17/2020] [Accepted: 03/11/2020] [Indexed: 11/02/2022] Open
Abstract
Roseburia and Eubacterium species of the human gut microbiota play an important role in the maintaince of human health, partly by producing butyrate, the main energy source of our colonic epithelial cells. However, our knowledge of the biochemistry and physiology of these bacteria has been limited by a lack of genetic manipulation techniques. Conjugative transposons previously introduced into Roseburia species could not be easily modified, greatly limiting their applicability as genetic modification platforms. Modular plasmid shuttle vectors have previously been developed for Clostridium species, which share a taxonomic order with Roseburia and Eubacterium, raising the possibility that these vectors could be used in these organisms. Here, we describe an optimized conjugation protocol enabling the transfer of autonomously replicating plasmids from an E. coli donor strain into Roseburia inulinivorans and Eubacterium rectale. The modular nature of the plasmids and their ability to be maintained in the recipient bacterium by autonomous replication makes them ideal for investigating heterologous gene expression, and as a platform for other genetic tools including antisense RNA silencing or mobile group II interon gene disruption strategies.
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Affiliation(s)
- Paul O Sheridan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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Scott KP. The impact of antimicrobials on gut bacteria: an interview with Karen Scott. Future Microbiol 2019; 14:1081-1082. [PMID: 31512517 DOI: 10.2217/fmb-2019-0221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Karen P Scott
- Gut Health Group, The Rowett Institute, University of Aberdeen King's College, Aberdeen, AB24 3FX, UK
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Scott KP, Grimaldi R, Cunningham M, Sarbini SR, Wijeyesekera A, Tang MLK, Lee JCY, Yau YF, Ansell J, Theis S, Yang K, Menon R, Arfsten J, Manurung S, Gourineni V, Gibson GR. Developments in understanding and applying prebiotics in research and practice-an ISAPP conference paper. J Appl Microbiol 2019; 128:934-949. [PMID: 31446668 DOI: 10.1111/jam.14424] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022]
Abstract
AIMS The concept of using specific dietary components to selectively modulate the gut microbiota to confer a health benefit, defined as prebiotics, originated in 1995. In 2018, a group of scientists met at the International Scientific Association for Probiotics and Prebiotics annual meeting in Singapore to discuss advances in the prebiotic field, focussing on issues affecting functionality, research methodology and geographical differences. METHODS AND RESULTS The discussion ranged from examining scientific literature supporting the efficacy of established prebiotics, to the prospects for establishing health benefits associated with novel compounds, isolated from different sources. CONCLUSIONS While many promising candidate prebiotics from across the globe have been highlighted in preliminary research, there are a limited number with both demonstrated mechanism of action and defined health benefits as required to meet the prebiotic definition. Prebiotics are part of a food industry with increasing market sales, yet there are great disparities in regulations in different countries. Identification and commercialization of new prebiotics with unique health benefits means that regulation must improve and remain up-to-date so as not to risk stifling research with potential health benefits for humans and other animals. SIGNIFICANCE AND IMPACT OF STUDY This summary of the workshop discussions indicates potential avenues for expanding the range of prebiotic substrates, delivery methods to enhance health benefits for the end consumer and guidance to better elucidate their activities in human studies.
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Affiliation(s)
- K P Scott
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - R Grimaldi
- Food and Nutritional Sciences, University of Reading, Reading, UK
| | - M Cunningham
- Metagenics (Aust) Pty Ltd., Virginia, Queensland, Australia
| | - S R Sarbini
- Department of Crop Science, Universiti Putra Malaysia, Bintulu Campus, Malaysia
| | - A Wijeyesekera
- Food and Nutritional Sciences, University of Reading, Reading, UK
| | - M L K Tang
- Department of Allergy and Immunology, The Royal Children's Hospital, Parkville, Melbourne, VIC, Australia
| | - J C-Y Lee
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Y F Yau
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - J Ansell
- Zespri International Ltd, Mt Maunganui, New Zealand
| | - S Theis
- Beneo-Institute, Obrigheim, Germany
| | - K Yang
- Departments of Obstetrics and Gynaecology and Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - R Menon
- The Bell Institute of Health and Nutrition, General Mills Inc., Minneapolis, MN, USA
| | - J Arfsten
- Nestlé Product and Technology Center Dairy, Konolfingen, Switzerland
| | - S Manurung
- Reckitt Benckiser, Nijmegen, The Netherlands
| | - V Gourineni
- Ingredion Incorporated, Bridgewater, NJ, USA
| | - G R Gibson
- Food and Nutritional Sciences, University of Reading, Reading, UK
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Sheridan PO, Martin JC, Minton NP, Flint HJ, O'Toole PW, Scott KP. Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids. Anaerobe 2019; 59:131-140. [PMID: 31228669 DOI: 10.1016/j.anaerobe.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/24/2019] [Accepted: 06/18/2019] [Indexed: 01/30/2023]
Abstract
Commensal butyrate-producing bacteria in the Firmicutes phylum are abundant in the human intestine and are important for maintaining health. However, understanding of the metabolism and host interaction of these bacteria is limited by the lack of genetic modification techniques. Here we establish a protocol enabling the transfer of autonomously-replicating shuttle vectors by conjugative plasmid transfer from an Escherichia coli donor into representatives of an important sub-group of strictly anaerobic human colonic Firmicutes. Five different plasmid shuttle vectors were tested, each carrying a different origin of replication from Gram-positive bacteria. Plasmid pMTL83151 (pCB102 replicon) were successfully transferred into two strains of Eubacterium rectale, while pMTL83151 and pMTL82151 (pBP1 replicon) were transferred into Roseburia inulinivorans A2-194. Plasmids that carried a Streptococcus bovis JB1 glycoside hydrolase family 16 β-(1,3-1,4)-glucanase gene were constructed and conjugated into Roseburia inulinivorans A2-194 and Eubacterium rectale T1-815, resulting in successful heterologous expression of this introduced enzymatic activity in these two strains of butyrate-producing Firmicutes.
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Affiliation(s)
- Paul O Sheridan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK; School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Nigel P Minton
- Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 2017; 35:1069-1076. [PMID: 28967887 DOI: 10.1038/nbt.3960] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
Abstract
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Eric Pelletier
- CEA - Institut François Jacob - Genoscope, Evry, France.,CNRS UMR-8030, Evry, France.,Université Evry Val d'Essonne, Evry, France
| | | | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Melanie Tramontano
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rajna Hercog
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris-Elias Jung
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthew R Hayward
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jillian R M Brown
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Michelle Daigneault
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.,Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruth Ann Luna
- Texas Children's Hospital, Feigin Center, Houston, Texas, USA
| | | | - Jana Junick
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Philippe Langella
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Céline Orvain
- CEA - Institut François Jacob - Genoscope, Evry, France
| | - Kiran Raosaheb Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Søren Persson
- Unit of Foodborne Infections, Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Delphine Saulnier
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Bhagirath Singh
- Centre for Human Immunology, Department of Microbiology & Immunology and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Kathleen Slezak
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Liping Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Joel Dore
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
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11
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Ashton JJ, Colquhoun CM, Cleary DW, Coelho T, Haggarty R, Mulder I, Batra A, Afzal NA, Beattie RM, Scott KP, Ennis S. 16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease. Medicine (Baltimore) 2017; 96:e7347. [PMID: 28658154 PMCID: PMC5500076 DOI: 10.1097/md.0000000000007347] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The human microbiome is of considerable interest to pediatric inflammatory bowel disease (PIBD) researchers with 1 potential mechanism for disease development being aberrant immune handling of the intestinal bacteria. This study analyses the fecal microbiome through treatment in newly diagnosed PIBD patients and compares to cohabiting siblings where possible. Patients were recruited on clinical suspicion of PIBD before diagnosis. Treatment-naïve fecal samples were collected, with further samples at 2 and 6 weeks into treatment. Samples underwent 16S ribosomal ribonucleic acid (RNA) gene sequencing and short-chain fatty acids (SCFAs) analysis, results were analyzed using quantitative-insights-into-microbial-ecology. Six PIBD patients were included in the cohort: 4 Crohn disease (CD), 1 ulcerative colitis (UC), 1 inflammatory bowel disease (IBD) unclassified, and median age 12.6 (range 10-15.1 years); 3 patients had an unaffected healthy sibling recruited. Microbial diversity (observed species/Chao1/Shannon diversity) was reduced in treatment-naïve patients compared to siblings and patients in remission. Principal coordinate analysis using Bray-Curtis dissimilarity and UniFrac revealed microbial shifts in CD over the treatment course. In treatment-naïve PIBD, there was reduction in functional ability for amino acid metabolism and carbohydrate handling compared to controls (P = .038) and patients in remission (P = .027). Metabolic function returned to normal after remission was achieved. SCFA revealed consistent detection of lactate in treatment-naïve samples. This study adds in-depth 16S rRNA sequencing analysis on a small longitudinal cohort to the literature and includes sibling controls and patients with UC/IBD unclassified. It highlights the initial dysbiosis, reduced diversity, altered functional potential, and subsequent shifts in bacteria from diagnosis over time to remission.
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Affiliation(s)
- James J. Ashton
- Department of Paediatric Gastroenterology, Southampton Children's Hospital
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton
| | | | - David W. Cleary
- Academic Unit of Clinical and Experimental Sciences, University of Southampton, Southampton
| | - Tracy Coelho
- Department of Paediatric Gastroenterology, Southampton Children's Hospital
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton
| | - Rachel Haggarty
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton
| | - Imke Mulder
- Gut Health Division, Rowett Institute, University of Aberdeen, Aberdeen
- 4D Pharma PLC, Aberdeen, UK
| | - Akshay Batra
- Department of Paediatric Gastroenterology, Southampton Children's Hospital
| | - Nadeem A. Afzal
- Department of Paediatric Gastroenterology, Southampton Children's Hospital
| | - R. Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital
| | - Karen P. Scott
- Gut Health Division, Rowett Institute, University of Aberdeen, Aberdeen
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton
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12
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Sheridan PO, Duncan SH, Walker AW, Scott KP, Louis P, Flint HJ. Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis. Int J Syst Evol Microbiol 2016; 66:2106. [PMID: 26916277 DOI: 10.1099/ijsem.0.000969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paul O Sheridan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Karen P Scott
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Petra Louis
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
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13
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O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043. [PMID: 28348841 PMCID: PMC5320581 DOI: 10.1099/mgen.0.000043] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022] Open
Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Affiliation(s)
- Paul O Sheridan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jennifer C Martin
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | - Hugh M B Harris
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Annick Bernalier-Donadille
- 4 Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France
| | - Sylvia H Duncan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Paul W O'Toole
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Karen P Scott
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
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14
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Hansen R, Scott KP, Khan S, Martin JC, Berry SH, Stevenson M, Okpapi A, Munro MJ, Hold GL. First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota. PLoS One 2015. [PMID: 26218283 PMCID: PMC4517813 DOI: 10.1371/journal.pone.0133320] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Considerable effort has been made to categorise the bacterial composition of the human gut and correlate findings with gastrointestinal disease. The infant gut has long been considered sterile at birth followed by rapid colonisation; however, this view has recently been challenged. We examined first-pass meconium from healthy term infants to confirm or refute sterility. Methods Healthy mothers were approached following vaginal delivery. First-pass meconium stools within 24 hours of delivery were obtained from healthy, breastfed infants with tight inclusion/exclusion criteria including rejecting any known antibiotic exposure - mother within 7 days preceding delivery or infant after birth. Stools were processed in triplicate for fluorescent in-situ hybridisation (FISH) with 16S rRNA-targeted probes including Bifidobacterium; Bacteroides-Prevotella; Lactobacillaceae/Enterococcaceae; Enterobacteriaceae; Streptococcaceae; Staphylococcaceae and Enterococcaceae. Absolute counts of all bacteria and proportional identification of each bacterial group were calculated. Confirmation of bacterial presence by PCR was undertaken on FISH-positive samples. Results The mothers of 31 newborn infants were recruited, 15 met inclusion/exclusion criteria and provided a sample within 24 hours of birth, processed in the lab within 4 hours. All babies were 37–40 weeks gestation. 8/15 were male, mean birth weight was 3.4kg and mean maternal age was 32 years. Meconium samples from 10/15 (66%) infants had evidence of bacteria based on FISH analysis. Of these, PCR was positive in only 1. Positive FISH counts ranged from 2.2 - 41.8 x 104 cells/g with a mean of 15.4 x 104 cells/g. (The limit of detection for automated counting is 106 cells/g). Cell counts were too low to allow formal diversity analysis. Amplification by PCR was not possible despite positive spiked samples demonstrating the feasibility of reaction. One baby was dominated by Enterobacteriaceae. The others contained 2-5 genera, with Bifidobacterium, Enterobacteriaceae, Enterococcaceae and Bacteroides-Prevotella the most prevalent. There was no association between bacterial counts and rupture of membrane duration, time to passage of meconium or time to lab. Conclusion This study provides evidence that low numbers of bacteria are present in first-pass meconium samples from healthy, vaginally-delivered, breastfed term infants. Only two-thirds of meconium samples had detectable bacteria, though at levels too low for automated counting or for reliable confirmation by PCR. This study suggests that gut bacterial colonisation is extremely limited at birth and occurs rapidly thereafter.
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Affiliation(s)
- Richard Hansen
- Department of Neonatology, Aberdeen Maternity Hospital, Aberdeen, United Kingdom
- Gastrointestinal Research Group, University of Aberdeen, Aberdeen, United Kingdom
| | - Karen P. Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Shoaib Khan
- Department of Neonatology, Aberdeen Maternity Hospital, Aberdeen, United Kingdom
| | - Jenny C. Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Susan H. Berry
- Gastrointestinal Research Group, University of Aberdeen, Aberdeen, United Kingdom
| | - Matthew Stevenson
- Gastrointestinal Research Group, University of Aberdeen, Aberdeen, United Kingdom
| | - Augusta Okpapi
- Department of Neonatology, Aberdeen Maternity Hospital, Aberdeen, United Kingdom
| | - Michael J. Munro
- Department of Neonatology, Aberdeen Maternity Hospital, Aberdeen, United Kingdom
| | - Georgina L. Hold
- Gastrointestinal Research Group, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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15
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Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice. Microbiome 2015; 3:26. [PMID: 26120470 PMCID: PMC4482049 DOI: 10.1186/s40168-015-0087-4] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/04/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several widely used molecular techniques were compared to establish the optimal methods to assess the bacterial composition in faecal samples from babies, before weaning. RESULTS The bacterial community profile detected in the faeces of infants is highly dependent on the methodology used. Bifidobacteria were the most abundant bacteria detected at 6 weeks in faeces from two initially breast-fed babies using fluorescent in situ hybridisation (FISH), in agreement with data from previous culture-based studies. Using the 16S rRNA gene sequencing approach, however, we found that the detection of bifidobacteria in particular crucially depended on the optimisation of the DNA extraction method, and the choice of primers used to amplify the V1-V3 regions of 16S rRNA genes prior to subsequent sequence analysis. Bifidobacteria were only well represented among amplified 16S rRNA gene sequences when mechanical disruption (bead-beating) procedures for DNA extraction were employed together with optimised "universal" PCR primers. These primers incorporate degenerate bases at positions where mismatches to bifidobacteria and other bacterial taxa occur. The use of a DNA extraction kit with no bead-beating step resulted in a complete absence of bifidobacteria in the sequence data, even when using the optimised primers. CONCLUSIONS This work emphasises the importance of sample processing methodology to downstream sequencing results and illustrates the value of employing multiple approaches for determining microbiota composition.
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Affiliation(s)
- Alan W. Walker
- />Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB UK
- />Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Jennifer C. Martin
- />Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB UK
| | - Paul Scott
- />Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Julian Parkhill
- />Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Harry J. Flint
- />Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB UK
| | - Karen P. Scott
- />Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB UK
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16
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Abstract
BACKGROUND The intestinal microbiota composition varies between healthy and diseased individuals for numerous diseases. Although any cause or effect relationship between the alterations in the gut microbiota and disease is not always clear, targeting the intestinal microbiota might offer new possibilities for prevention and/or treatment of disease. OBJECTIVE Here we review some examples of manipulating the intestinal microbiota by prebiotics, probiotics, and fecal microbial transplants. RESULTS Prebiotics are best known for their ability to increase the number of bifidobacteria. However, specific prebiotics could potentially also stimulate other species they can also stimulate other species associated with health, like Akkermansia muciniphila, Ruminococcus bromii, the Roseburia/Enterococcus rectale group, and Faecalibacterium prausnitzii. Probiotics have beneficial health effects for different diseases and digestive symptoms. These effects can be due to the direct effect of the probiotic bacterium or its products itself, as well as effects of the probiotic on the resident microbiota. Probiotics can influence the microbiota composition as well as the activity of the resident microbiota. Fecal microbial transplants are a drastic intervention in the gut microbiota, aiming for total replacement of one microbiota by another. With numerous successful studies related to antibiotic-associated diarrhea and Clostridium difficile infection, the potential of fecal microbial transplants to treat other diseases like inflammatory bowel disease, irritable bowel syndrome, and metabolic and cardiovascular disorders is under investigation. CONCLUSIONS Improved knowledge on the specific role of gut microbiota in prevention and treatment of disease will help more targeted manipulation of the intestinal microbiota. Further studies are necessary to see the (long term) effects for health of these interventions.
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Affiliation(s)
- Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Tore Midtvedt
- Department of Microbiology, Tumor and Cell Biology (MTC) Karolinska Institute, Stockholm, Sweden
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17
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Reichardt N, Duncan SH, Young P, Belenguer A, McWilliam Leitch C, Scott KP, Flint HJ, Louis P. Erratum: Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J 2014. [DOI: 10.1038/ismej.2014.48] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Sheridan PO, Bindels LB, Saulnier DM, Reid G, Nova E, Holmgren K, O'Toole PW, Bunn J, Delzenne N, Scott KP. Can prebiotics and probiotics improve therapeutic outcomes for undernourished individuals? Gut Microbes 2014; 5:74-82. [PMID: 24637591 PMCID: PMC4049942 DOI: 10.4161/gmic.27252] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
It has become clear in recent years that the human intestinal microbiota plays an important role in maintaining health and thus is an attractive target for clinical interventions. Scientists and clinicians have become increasingly interested in assessing the ability of probiotics and prebiotics to enhance the nutritional status of malnourished children, pregnant women, the elderly, and individuals with non-communicable disease-associated malnutrition. A workshop was held by the International Scientific Association for Probiotics and Prebiotics (ISAPP), drawing on the knowledge of experts from industry, medicine, and academia, with the objective to assess the status of our understanding of the link between the microbiome and under-nutrition, specifically in relation to probiotic and prebiotic treatments for under-nourished individuals. These discussions led to four recommendations: (1) The categories of malnourished individuals need to be differentiated To improve treatment outcomes, subjects should first be categorized based on the cause of malnutrition, additional health-concerns, differences in the gut microbiota, and sociological considerations. (2) Define a baseline "healthy" gut microbiota for each category Altered nutrient requirement (for example, in pregnancy and old age) and individual variation may change what constitutes a healthy gut microbiota for the individual. (3) Perform studies using model systems to test the effectiveness of potential probiotics and prebiotics against these specific categories These should illustrate how certain microbiota profiles can be altered, as members of different categories may respond differently to the same treatment. (4) Perform robust well-designed human studies with probiotics and/or prebiotics, with appropriate, defined primary outcomes and sample size These are critical to show efficacy and understand responder and non-responder outcomes. It is hoped that these recommendations will lead to new approaches that combat malnutrition. This report is the result of discussion during an expert workshop titled "How do the microbiota and probiotics and/or prebiotics influence poor nutritional status?" held during the 10th Meeting of the International Scientific Association for Probiotics and Prebiotics (ISAPP) in Cork, Ireland from October 1-3, 2012. The complete list of workshop attendees is shown in Table 1.
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Affiliation(s)
- Paul O Sheridan
- Rowett Institute of Nutrition and Health; University of Aberdeen; Aberdeen, UK,Department of Microbiology & Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
| | - Laure B Bindels
- Louvain Drug Research Institute; Université Catholique de Louvain; Brussels, Belgium
| | | | - Gregor Reid
- Lawson Health Research Institute; London, ON Canada
| | - Esther Nova
- Institute of Food Science; Technology and Nutrition (ICTAN)-CSIC; Madrid, Spain
| | | | - Paul W O'Toole
- Department of Microbiology & Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
| | - James Bunn
- Alder Hey Childrens NHS Foundation Trust; Eaton Road; Liverpool, UK
| | - Nathalie Delzenne
- Louvain Drug Research Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Karen P Scott
- Rowett Institute of Nutrition and Health; University of Aberdeen; Aberdeen, UK,Correspondence to: Karen P Scott,
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19
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Scott KP, Martin JC, Duncan SH, Flint HJ. Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. FEMS Microbiol Ecol 2013; 87:30-40. [PMID: 23909466 DOI: 10.1111/1574-6941.12186] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/23/2013] [Accepted: 07/29/2013] [Indexed: 01/27/2023] Open
Abstract
Dietary macronutrients affect the composition of the gut microbiota, and prebiotics are used to improve and maintain a healthy gut. The impact of prebiotics on dominant gut bacteria other than bifidobacteria, however, is under-researched. Here, we report carbohydrate utilisation patterns for representative butyrate-producing anaerobes, belonging to the Gram-positive Firmicutes families Lachnospiraceae and Ruminococcaceae, by comparison with selected Bacteroides and Bifidobacterium species. Growth assessments using anaerobic Hungate tubes and a new rapid microtitre plate assay were generally in good agreement. The Bacteroides strains tested showed some growth on basal medium with no added carbohydrates, utilising peptides in the growth medium. The butyrate-producing strains exhibited different growth profiles on the substrates, which included starch, inulin, fructooligosaccharides (FOS), galactooligosaccharides (GOS) and xylooligosaccharides (XOS). Eleven were able to grow on short-chain FOS, but this number decreased as the chain length of the fructan substrates increased. Long-chain inulin was utilised by Roseburia inulinivorans, but by none of the Bifidobacterium species examined here. XOS was a more selective growth substrate than FOS, with only six of the 11 Firmicutes strains able to use XOS for growth. These results illustrate the selectivity of different prebiotics and help to explain why some are butyrogenic.
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Affiliation(s)
- Karen P Scott
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, UK
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20
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Neville BA, Sheridan PO, Harris HMB, Coughlan S, Flint HJ, Duncan SH, Jeffery IB, Claesson MJ, Ross RP, Scott KP, O'Toole PW. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans. PLoS One 2013; 8:e68919. [PMID: 23935906 PMCID: PMC3720852 DOI: 10.1371/journal.pone.0068919] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/03/2013] [Indexed: 02/06/2023] Open
Abstract
Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute “cell motility” category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13–4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved metagenome assembly from short reads will be required to facilitate in silico analyses of complete complex biochemical pathways for low-abundance target species from shotgun metagenomes.
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Affiliation(s)
- B. Anne Neville
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Paul O. Sheridan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | | | - Simone Coughlan
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Harry J. Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Sylvia H. Duncan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Ian B. Jeffery
- Department of Microbiology, University College Cork, Cork, Ireland
| | | | - R. Paul Ross
- Teagasc Moorepark Food Research Centre, Fermoy, County Cork, Ireland
| | - Karen P. Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Paul W. O'Toole
- Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail:
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21
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Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH. The influence of diet on the gut microbiota. Pharmacol Res 2012; 69:52-60. [PMID: 23147033 DOI: 10.1016/j.phrs.2012.10.020] [Citation(s) in RCA: 616] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/15/2012] [Accepted: 10/29/2012] [Indexed: 02/06/2023]
Abstract
Diet is a major factor driving the composition and metabolism of the colonic microbiota. The amount, type and balance of the main dietary macronutrients (carbohydrates, proteins and fats) have a great impact on the large intestinal microbiota. The human colon contains a dense population of bacterial cells that outnumber host cells 10-fold. Bacteroidetes, Firmicutes and Actinobacteria are the three major phyla that inhabit the human large intestine and these bacteria possess a fascinating array of enzymes that can degrade complex dietary substrates. Certain colonic bacteria are able to metabolise a remarkable variety of substrates whilst other species carry out more specialised activities, including primary degradation of plant cell walls. Microbial metabolism of dietary carbohydrates results mainly in the formation of short chain fatty acids and gases. The major bacterial fermentation products are acetate, propionate and butyrate; and the production of these tends to lower the colonic pH. These weak acids influence the microbial composition and directly affect host health, with butyrate the preferred energy source for the colonocytes. Certain bacterial species in the colon survive by cross-feeding, using either the breakdown products of complex carbohydrate degradation or fermentation products such as lactic acid for growth. Microbial protein metabolism results in additional fermentation products, some of which are potentially harmful to host health. The current 'omic era promises rapid progress towards understanding how diet can be used to modulate the composition and metabolism of the gut microbiota, allowing researchers to provide informed advice, that should improve long-term health status.
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Affiliation(s)
- Karen P Scott
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK.
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22
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Bindels LB, Porporato P, Dewulf EM, Verrax J, Neyrinck AM, Martin JC, Scott KP, Buc Calderon P, Feron O, Muccioli GG, Sonveaux P, Cani PD, Delzenne NM. Gut microbiota-derived propionate reduces cancer cell proliferation in the liver. Br J Cancer 2012; 107:1337-44. [PMID: 22976799 PMCID: PMC3494429 DOI: 10.1038/bjc.2012.409] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: Metabolites released by the gut microbiota may influence host metabolism and immunity. We have tested the hypothesis that inulin-type fructans (ITF), by promoting microbial production of short-chain fatty acids (SCFA), influence cancer cell proliferation outside the gut. Methods: Mice transplanted with Bcr-Abl-transfected BaF3 cells, received ITF in their drinking water. Gut microbiota was analysed by 16S rDNA polymerase chain reaction (PCR)–denaturing gradient gel electrophoresis (DGGE) and qPCR. Serum Short-chain fatty acids were quantified by UHPLC-MS. Cell proliferation was evaluated in vivo, by molecular biology and histology, and in vitro. Results: Inulin-type fructans treatment reduces hepatic BaF3 cell infiltration, lessens inflammation and increases portal propionate concentration. In vitro, propionate reduces BaF3 cell growth through a cAMP level-dependent pathway. Furthermore, the activation of free fatty acid receptor 2 (FFA2), a Gi/Gq-protein-coupled receptor also known as GPR43 and that binds propionate, lessens the proliferation of BaF3 and other human cancer cell lines. Conclusion: We show for the first time that the fermentation of nutrients such as ITF into propionate can counteract malignant cell proliferation in the liver tissue. Our results support the interest of FFA2 activation as a new strategy for cancer therapeutics. This study highlights the importance of research focusing on gut microbes–host interactions for managing systemic and severe diseases such as leukaemia.
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Affiliation(s)
- L B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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23
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Abstract
Bacteria that colonize the mammalian intestine collectively possess a far larger repertoire of degradative enzymes and metabolic capabilities than their hosts. Microbial fermentation of complex non-digestible dietary carbohydrates and host-derived glycans in the human intestine has important consequences for health. Certain dominant species, notably among the Bacteroidetes, are known to possess very large numbers of genes that encode carbohydrate active enzymes and can switch readily between different energy sources in the gut depending on availability. Nevertheless, more nutritionally specialized bacteria appear to play critical roles in the community by initiating the degradation of complex substrates such as plant cell walls, starch particles and mucin. Examples are emerging from the Firmicutes, Actinobacteria and Verrucomicrobium phyla, but more information is needed on these little studied groups. The impact of dietary carbohydrates, including prebiotics, on human health requires understanding of the complex relationship between diet composition, the gut microbiota and metabolic outputs.
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Affiliation(s)
- Harry J. Flint
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK,Correspondence to: Harry J. Flint,
| | - Karen P. Scott
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK
| | - Sylvia H. Duncan
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK
| | - Petra Louis
- Rowett Institute of Nutrition and Health; University of Aberdeen; Bucksburn, Aberdeen UK
| | - Evelyne Forano
- INRA; UR454 Microbiologie; Saint-Genès Champanelle, France
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24
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Bindels LB, Beck R, Schakman O, Martin JC, De Backer F, Sohet FM, Dewulf EM, Pachikian BD, Neyrinck AM, Thissen JP, Verrax J, Calderon PB, Pot B, Grangette C, Cani PD, Scott KP, Delzenne NM. Restoring specific lactobacilli levels decreases inflammation and muscle atrophy markers in an acute leukemia mouse model. PLoS One 2012; 7:e37971. [PMID: 22761662 PMCID: PMC3384645 DOI: 10.1371/journal.pone.0037971] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/27/2012] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota has recently been proposed as a novel component in the regulation of host homeostasis and immunity. We have assessed for the first time the role of the gut microbiota in a mouse model of leukemia (transplantation of BaF3 cells containing ectopic expression of Bcr-Abl), characterized at the final stage by a loss of fat mass, muscle atrophy, anorexia and inflammation. The gut microbial 16S rDNA analysis, using PCR-Denaturating Gradient Gel Electrophoresis and quantitative PCR, reveals a dysbiosis and a selective modulation of Lactobacillus spp. (decrease of L. reuteri and L. johnsonii/gasseri in favor of L. murinus/animalis) in the BaF3 mice compared to the controls. The restoration of Lactobacillus species by oral supplementation with L. reuteri 100-23 and L. gasseri 311476 reduced the expression of atrophy markers (Atrogin-1, MuRF1, LC3, Cathepsin L) in the gastrocnemius and in the tibialis, a phenomenon correlated with a decrease of inflammatory cytokines (interleukin-6, monocyte chemoattractant protein-1, interleukin-4, granulocyte colony-stimulating factor, quantified by multiplex immuno-assay). These positive effects are strain- and/or species-specific since L. acidophilus NCFM supplementation does not impact on muscle atrophy markers and systemic inflammation. Altogether, these results suggest that the gut microbiota could constitute a novel therapeutic target in the management of leukemia-associated inflammation and related disorders in the muscle.
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Affiliation(s)
- Laure B. Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Raphaël Beck
- Toxicology and Cancer Biology Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Olivier Schakman
- Laboratory of Cell Physiology, Institute Of NeuroScience, Université catholique de Louvain, Brussels, Belgium
| | - Jennifer C. Martin
- Gut Health Division, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Fabienne De Backer
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Florence M. Sohet
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Evelyne M. Dewulf
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Barbara D. Pachikian
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Audrey M. Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Jean-Paul Thissen
- Departement of Diabetology and Nutrition, Institut de recherche expérimentale et clinique, Université catholique de Louvain, Brussels, Belgium
| | - Julien Verrax
- Toxicology and Cancer Biology Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Pedro Buc Calderon
- Toxicology and Cancer Biology Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Bruno Pot
- Lactic Acid Bacteria and Mucosal Immunity, Center for Infection and Immunity of Lille, INSERM U1019-CNRS UMR 8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Corinne Grangette
- Lactic Acid Bacteria and Mucosal Immunity, Center for Infection and Immunity of Lille, INSERM U1019-CNRS UMR 8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Patrice D. Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Karen P. Scott
- Gut Health Division, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Nathalie M. Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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Cernat RC, Scott KP. Evaluation of novel assays to assess the influence of different iron sources on the growth of Clostridium difficile. Anaerobe 2012; 18:298-304. [PMID: 22554901 DOI: 10.1016/j.anaerobe.2012.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/14/2012] [Accepted: 04/16/2012] [Indexed: 01/05/2023]
Abstract
The ability of four Clostridium difficile strains to utilize various exogenous organic and inorganic iron sources for growth under iron-depleted (250 μM DPP) and iron-limited (75 μM DPP) conditions was analyzed in liquid broth cultures grown in tubes and in microtiter plates, and data compared with results from a bioassay developed on solid media. The growth profile of C. difficile varied depending on the iron source and availability. Addition of FeSO(4), FeCl(3), Fe citrate and ferritin allowed growth in an iron-depleted environment whereas glycoproteins (iron-saturated and low-iron lactoferrin, apo- and holo-transferrin) and heme proteins (hemoglobin, hematin and hemin) did not. All iron sources, except lactoferrin, were able to restore bacterial growth under iron-limited conditions to varying extents. The results demonstrated that the broth microtiter assay developed here was reproducible, reliable and convenient for high-throughput analysis of the growth of C. difficile compared to alternative traditional methods.
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Affiliation(s)
- Ramona C Cernat
- Microbial Ecology, Gut Health Division, Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, UK
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26
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Chassard C, Dapoigny M, Scott KP, Crouzet L, Del'homme C, Marquet P, Martin JC, Pickering G, Ardid D, Eschalier A, Dubray C, Flint HJ, Bernalier-Donadille A. Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome. Aliment Pharmacol Ther 2012; 35:828-38. [PMID: 22315951 DOI: 10.1111/j.1365-2036.2012.05007.x] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 09/20/2011] [Accepted: 01/12/2012] [Indexed: 12/08/2022]
Abstract
BACKGROUND The role of the gut microbiota in patho-physiology of irritable bowel syndrome (IBS) is suggested by several studies. However, standard cultural and molecular methods used to date have not revealed specific and consistent IBS-related groups of microbes. AIM To explore the constipated-IBS (C-IBS) gut microbiota using a function-based approach. METHODS The faecal microbiota from 14 C-IBS women and 12 sex-match healthy subjects were examined through a combined strictly anaerobic cultural evaluation of functional groups of microbes and fluorescent in situ hybridisation (16S rDNA gene targeting probes) to quantify main groups of bacteria. Starch fermentation by C-IBS and healthy faecal samples was evaluated in vitro. RESULTS In C-IBS, the numbers of lactate-producing and lactate-utilising bacteria and the number of H(2) -consuming populations, methanogens and reductive acetogens, were at least 10-fold lower (P < 0.05) compared with control subjects. Concomitantly, the number of lactate- and H(2) -utilising sulphate-reducing population was 10 to 100 fold increased in C-IBS compared with healthy subjects. The butyrate-producing Roseburia - E. rectale group was in lower number (0.01 < P < 0.05) in C-IBS than in control. C-IBS faecal microbiota produced more sulphides and H(2) and less butyrate from starch fermentation than healthy ones. CONCLUSIONS A major functional dysbiosis was observed in constipated-irritable bowel syndrome gut microbiota, reflecting altered intestinal fermentation. Sulphate-reducing population increased in the gut of C-IBS and were accompanied by alterations in other microbial groups. This could be responsible for changes in the metabolic output and enhancement in toxic sulphide production which could in turn influence gut physiology and contribute to IBS pathogenesis.
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Affiliation(s)
- C Chassard
- INRA, UR Microbiology Unit, Clermont-Ferrand Research Centre, Saint Genès-Champanelle, France
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Minas K, McEwan NR, Newbold CJ, Scott KP. Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures. FEMS Microbiol Lett 2011; 325:162-9. [DOI: 10.1111/j.1574-6968.2011.02424.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Konstantinos Minas
- Institute for Innovation Design and Sustainability; Robert Gordon University; Aberdeen; UK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural Sciences; Aberystwyth University; Aberystwyth; UK
| | - Charles Jamie Newbold
- Institute of Biological Environmental and Rural Sciences; Aberystwyth University; Aberystwyth; UK
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28
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Gibson GR, Scott KP, Rastall RA, Tuohy KM, Hotchkiss A, Dubert-Ferrandon A, Gareau M, Murphy EF, Saulnier D, Loh G, Macfarlane S, Delzenne N, Ringel Y, Kozianowski G, Dickmann R, Lenoir-Wijnkoop I, Walker C, Buddington R. Dietary prebiotics: current status and new definition. ACTA ACUST UNITED AC 2010. [DOI: 10.1616/1476-2137.15880] [Citation(s) in RCA: 319] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Seville LA, Patterson AJ, Scott KP, Mullany P, Quail MA, Parkhill J, Ready D, Wilson M, Spratt D, Roberts AP. Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA. Microb Drug Resist 2009; 15:159-66. [PMID: 19728772 DOI: 10.1089/mdr.2009.0916] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We have analyzed the total metagenomic DNA from both human oral and fecal samples derived from healthy volunteers from six European countries to determine the molecular basis for tetracycline and erythromycin resistance. We have determined that tet(M) and tet(W) are the most prevalent tetracycline resistance genes assayed for in the oral and fecal metagenomes, respectively. Additionally, tet(Q), tet(O), and tet(O/32/O) have been shown to be common. We have also shown that erm(B), erm(V), and erm(E) are common erythromycin resistance genes present in these environments. Further, we have demonstrated the ubiquitous presence of the Tn916 integrase in the oral metagenomes and the Tn4451 and Tn1549 integrase genes within the fecal metagenomes.
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Affiliation(s)
- Lorna A Seville
- Division of Microbial Diseases, UCL Eastman Dental Institute, London, United Kingdom
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30
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Chassard C, Scott KP, Marquet P, Martin JC, Del'homme C, Dapoigny M, Flint HJ, Bernalier-Donadille A. Assessment of metabolic diversity within the intestinal microbiota from healthy humans using combined molecular and cultural approaches. FEMS Microbiol Ecol 2008; 66:496-504. [PMID: 18811647 DOI: 10.1111/j.1574-6941.2008.00595.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The human gut harbours a wide range of bacterial communities that play key roles in supplying nutrients and energy to the host through anaerobic fermentation of dietary components and host secretions. This fermentative process involves different functional groups of microorganisms linked in a trophic chain. Although the diversity of the intestinal microbiota has been studied extensively using molecular techniques, the functional aspects of this biodiversity remain mostly unexplored. The aim of the present work was to enumerate the principal metabolic groups of microorganisms involved in the fermentative process in the gut of healthy humans. These functional groups of microorganisms were quantified by a cultural approach, while the taxonomic composition of the microbiota was assessed by in situ hybridization on the same faecal samples. The functional groups of microorganisms that predominated in the gut were the polysaccharide-degrading populations involved in the breakdown of the most readily available exogenous and endogenous substrates and the predominant butyrate-producing species. Most of the functional groups of microorganisms studied appeared to be present at rather similar levels in all healthy volunteers, suggesting that optimal numbers of these various bacterial groups are crucial for efficient gut fermentation, as well as for host nutrition and health. Significant interindividual differences were, however, confirmed with respect to the numbers of methanogenic archaea, filter paper-degrading and acetogenic bacteria and the products formed by lactate-utilizing bacteria.
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Affiliation(s)
- Christophe Chassard
- INRA, Unité de Microbiologie UR 454, Centre de Recherches de Clermont-Ferrand-Theix, Saint Genès-Champanelle, France
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31
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Abstract
Recent analyses of ribosomal RNA sequence diversity have demonstrated the extent of bacterial diversity in the human colon, and have provided new tools for monitoring changes in the composition of the gut microbial community. There is now an excellent opportunity to correlate ecological niches and metabolic activities with particular phylogenetic groups among the microbiota of the human gut. Bacteria that associate closely with particulate material and surfaces in the gut include specialized primary degraders of insoluble substrates, including resistant starch, plant structural polysaccharides and mucin. Butyrate-producing bacteria found in human faeces belong mainly to the clostridial clusters IV and XIVa. In vitro and in vivo evidence indicates that a group related to Roseburia and Eubacterium rectale plays a major role in mediating the butyrogenic effect of fermentable dietary carbohydrates. Additional cluster XIVa species can convert lactate to butyrate, while some members of the clostridial cluster IX convert lactate to propionate. The metabolic outputs of the gut microbial community depend not only on available substrate, but also on the gut environment, with pH playing a major role. Better understanding of the colonic microbial ecosystem will help to explain and predict the effects of dietary additives, including nondigestible carbohydrates, probiotics and prebiotics.
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Affiliation(s)
- P Louis
- Microbial Ecology Group, Rowett Research Institute, Aberdeen, UK
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32
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Abstract
The microbiota of the human intestinal tract play an important role in health, in particular by mediating many of the effects of diet upon gut health. Surveys of 16S rRNA sequence diversity in the human colon have emphasized the low proportion of sequences that match cultured bacterial species. This may reflect limited recent effort on cultivation rather than inherent unculturability, however, as anaerobic isolation methods can apparently recover a wide range of the diversity found. A combination of information from representative cultures, molecular tools for enumeration and tracking of bacterial metabolites offers the most powerful route to understanding the roles played by different groups of bacteria in the gut ecosystem. Progress is being made for example in defining key functional groups including primary colonizers of insoluble dietary substrates, and major contributors to metabolites such as butyrate that influence the health of the gut mucosa. There is increasing evidence that bacterial populations in the large intestine respond to changes in diet, in particular to the type and quantity of dietary carbohydrate. A general consequence of increased carbohydrate consumption is to reduce the pH of the gut lumen, which is likely to play a major role in determining bacterial metabolism and competition. Oligosaccharides used as dietary prebiotics must inevitably have complex effects upon the bacterial community that include non-target organisms and the consequences of metabolic cross-feeding and changes in the gut environment.
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Affiliation(s)
- Harry J Flint
- Microbial Ecology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB219SB, UK.
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Patterson AJ, Colangeli R, Spigaglia P, Scott KP. Distribution of specific tetracycline and erythromycin resistance genes in environmental samples assessed by macroarray detection. Environ Microbiol 2007; 9:703-15. [PMID: 17298370 DOI: 10.1111/j.1462-2920.2006.01190.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A macroarray system was developed to screen environmental samples for the presence of specific tetracycline (Tc(R)) and erythromycin (erm(R)) resistance genes. The macroarray was loaded with polymerase chain reaction (PCR) amplicons of 23 Tc(R) genes and 10 erm(R) genes. Total bacterial genomic DNA was extracted from soil and animal faecal samples collected from different European countries. Macroarray hybridization was performed under stringent conditions and the results were analysed by fluorescence scanning. Pig herds in Norway, reared without antibiotic use, had a significantly lower incidence of antibiotic resistant bacteria than those reared in other European countries, and organic herds contained lower numbers of resistant bacteria than intensively farmed animals. The relative proportions of the different genes were constant across the different countries. Ribosome protection type Tc(R) genes were the most common resistance genes in animal faecal samples, with the tet(W) gene the most abundant, followed by tet(O) and tet(Q). Different resistance genes were present in soil samples, where erm(V) and erm(E) were the most prevalent followed by the efflux type Tc(R) genes. The macroarray proved a powerful tool to screen DNA extracted from environmental samples to identify the most abundant Tc(R) and erm(R) genes within those tested, avoiding the need for culturing and biased PCR amplification steps.
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Affiliation(s)
- Andrea J Patterson
- Gut Health Division, Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, UK
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34
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Ramsay AG, Scott KP, Martin JC, Rincon MT, Flint HJ. Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon. Microbiology (Reading) 2007; 152:3281-3290. [PMID: 17074899 DOI: 10.1099/mic.0.29233-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Selected butyrate-producing bacteria from the human colon that are related to Roseburia spp. and Butyrivibrio fibrisolvens showed a good ability to utilize a variety of starches for growth when compared with the Gram-negative amylolytic anaerobe Bacteroides thetaiotaomicron. A major cell-associated amylase of high molecular mass (140-210 kDa) was detected in each strain by SDS-PAGE zymogram analysis, and genes corresponding to these enzymes were analysed for two representative strains. Amy13B from But. fibrisolvens 16/4 is a multi-domain enzyme of 144.6 kDa that includes a family 13 glycoside hydrolase domain, and duplicated family 26 carbohydrate-binding modules. Amy13A (182.4 kDa), from Roseburia inulinivorans A2-194, also includes a family 13 domain, which is preceded by two repeat units of approximately 116 aa rich in aromatic residues, an isoamylase N-terminal domain, a pullulanase-associated domain, and an additional unidentified domain. Both Amy13A and Amy13B have N-terminal signal peptides and C-terminal cell-wall sorting signals, including a modified LPXTG motif similar to that involved in interactions with the cell surface in other Gram-positive bacteria, a hydrophobic transmembrane segment, and a basic C terminus. The overexpressed family 13 domains showed an absolute requirement for Mg2+ or Ca2+ for activity, and functioned as 1,4-alpha-glucanohydrolases (alpha-amylases; EC 3.2.1.1). These major starch-degrading enzymes thus appear to be anchored to the cell wall in this important group of human gut bacteria.
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Affiliation(s)
- Alan G Ramsay
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Karen P Scott
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jenny C Martin
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Marco T Rincon
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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35
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Saarela M, Maukonen J, von Wright A, Vilpponen-Salmela T, Patterson AJ, Scott KP, Hämynen H, Mättö J. Tetracycline susceptibility of the ingested Lactobacillus acidophilus LaCH-5 and Bifidobacterium animalis subsp. lactis Bb-12 strains during antibiotic/probiotic intervention. Int J Antimicrob Agents 2007; 29:271-80. [PMID: 17207972 DOI: 10.1016/j.ijantimicag.2006.09.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 09/26/2006] [Accepted: 09/26/2006] [Indexed: 01/07/2023]
Abstract
We investigated the effects of oral therapy with doxycycline, a tetracycline group antibiotic, on the gastrointestinal (GI) survival and tetracycline susceptibility of probiotic strains Lactobacillus acidophilus LaCH-5 and Bifidobacterium animalis subsp. lactis Bb-12. In addition, the influence of doxycycline therapy on the diversity of the predominant faecal microbiota was evaluated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Faecal samples from the antibiotic group (receiving antibiotics and probiotics) and the control group (receiving probiotics only) were analysed for anaerobically and aerobically growing bacteria, bifidobacteria and lactic acid bacteria as well as for the dominant microbiota. Although doxycycline consumption did not have a large impact on GI survival of the probiotics, it had a detrimental effect on the bifidobacteria and on the diversity of the dominant faecal microbiota. A higher proportion of tetracycline-resistant anaerobically growing bacteria and bifidobacteria was detected in the antibiotic group than in the control group. Several antibiotic group subjects had faecal B. animalis subsp. lactis Bb-12-like isolates with reduced tetracycline susceptibility. This was unlikely to be due to the acquisition of novel tetracycline resistance determinants, since only tet(W), which is also present in the ingested B. animalis subsp. lactis Bb-12, was found in the resistant isolates. Thus, concomitant ingestion of probiotic L. acidophilus LaCH-5 and B. animalis subsp. lactis Bb-12 with the antibiotic did not generate a safety risk regarding the possible GI transfer of tetracycline resistance genes to the ingested strains.
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Affiliation(s)
- Maria Saarela
- VTT, Biotechnology, P.O. Box 1000, FI-02044 VTT, Finland.
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Affiliation(s)
- Katarzyna A Kazimierczak
- Microbial Ecology, Gut Health Division, Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, Scotland, United Kingdom
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Patterson AJ, Rincon MT, Flint HJ, Scott KP. Mosaic tetracycline resistance genes are widespread in human and animal fecal samples. Antimicrob Agents Chemother 2006; 51:1115-8. [PMID: 17178791 PMCID: PMC1803118 DOI: 10.1128/aac.00725-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mosaic tetracycline resistance genes comprising tet(O), tet(W), and tet(32) sequences were abundant in DNA extracted from pig and human fecal samples, accounting for 78% (50/64) and 46% (37/80) of genes amplified with a tet(O) primer set, respectively, in two samples. The nonmosaic tet(32) gene was isolated from a human saliva bacterium.
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Affiliation(s)
- Andrea J Patterson
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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Duncan SH, Aminov RI, Scott KP, Louis P, Stanton TB, Flint HJ. Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces. Int J Syst Evol Microbiol 2006; 56:2437-2441. [PMID: 17012576 DOI: 10.1099/ijs.0.64098-0] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences to Roseburia intestinalis L1-82(T) (DSM 14610(T)), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0.5x1.5-5.0 mum and were motile. Two strains belonging to one cluster (A2-181 and A2-183(T)) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1(T)) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194(T)) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1(T) gave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representative Roseburia strains A2-183(T), A2-194(T), M72/1(T) and R. intestinalis L1-82(T) were 47.4, 41.4, 42.0 and 42.6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novel Roseburia species are proposed, with the names Roseburia hominis sp. nov. (type strain A2-183(T)=DSM 16839(T)=NCIMB 14029(T)), Roseburia inulinivorans sp. nov. (type strain A2-194(T)=DSM 16841(T)=NCIMB 14030(T)) and Roseburia faecis sp. nov. (type strain M72/1(T)=DSM 16840(T)=NCIMB 14031(T)).
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Affiliation(s)
- Sylvia H Duncan
- Gut Health Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Rustam I Aminov
- Gut Health Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Karen P Scott
- Gut Health Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Petra Louis
- Gut Health Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Thaddeus B Stanton
- National Animal Disease Center, USDA ARS, PO Box 70, 2300 Dayton Road, Ames, IA 50010, USA
| | - Harry J Flint
- Gut Health Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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Kazimierczak KA, Flint HJ, Scott KP. Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria. Antimicrob Agents Chemother 2006; 50:2632-9. [PMID: 16870752 PMCID: PMC1538676 DOI: 10.1128/aac.01587-05] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
tet(W) is one of the most abundant tetracycline resistance genes found in bacteria from the mammalian gut and was first identified in the rumen anaerobe Butyrivibrio fibrisolvens 1.230, where it is highly mobile and its transfer is associated with the transposable chromosomal element TnB1230. In order to compare the genetic basis for tet(W) carriage in different bacteria, we studied sequences flanking tet(W) in representatives of seven bacterial genera originating in diverse gut environments. The sequences 657 bp upstream and 43 bp downstream of tet(W) were 96 to 100% similar in all strains examined. A common open reading frame (ORF) was identified downstream of tet(W) in five different bacteria, while another conserved ORF that flanked tet(W) in B. fibrisolvens 1.230 was also present upstream of tet(W) in a human colonic Roseburia isolate and in another rumen B. fibrisolvens isolate. In one species, Bifidobacterium longum (strain F8), a novel transposase was located within the conserved 657-bp region upstream of tet(W) and was flanked by imperfect direct repeats. Additional direct repeats 6 bp long were identified on each end of a chromosomal ORF interrupted by the insertion of the putative transposase and the tet(W) gene. This tet(W) gene was transferable at low frequencies between Bifidobacterium strains. A putative minielement carrying a copy of tet(W) was identified in B. fibrisolvens transconjugants that had acquired the tet(W) gene on TnB1230. Several different mechanisms, including mechanisms involving plasmids and conjugative transposons, appear to be involved in the horizontal transfer of tet(W) genes, but small core regions that may function as minielements are conserved.
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Scott KP, Martin JC, Campbell G, Mayer CD, Flint HJ. Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "Roseburia inulinivorans". J Bacteriol 2006; 188:4340-9. [PMID: 16740940 PMCID: PMC1482943 DOI: 10.1128/jb.00137-06] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
"Roseburia inulinivorans" is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin. R. inulinivorans A2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. A shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in changing from glucose to fucose utilization. This revealed a set of genes coding for fucose utilization, propanediol utilization, and the formation of propionate and propanol that are up-regulated during growth on fucose. These include homologues of genes that are implicated in polyhedral body formation in Salmonella enterica. Dehydration of the intermediate 1,2-propanediol involves an enzyme belonging to the new B12-independent glycerol dehydratase family, in contrast to S. enterica, which relies on a B12-dependent enzyme. A typical gram-positive agr-type quorum-sensing system was also up-regulated in R. inulinivorans during growth on fucose. Despite the lack of genome sequence information for this commensal bacterium, microarray analysis has provided a powerful tool for obtaining new information on its metabolic capabilities.
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Affiliation(s)
- Karen P Scott
- Gut Health Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, United Kingdom.
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Melville CM, Brunel R, Flint HJ, Scott KP. The Butyrivibrio fibrisolvens tet(W) gene is carried on the novel conjugative transposon TnB1230, which contains duplicated nitroreductase coding sequences. J Bacteriol 2004; 186:3656-9. [PMID: 15150255 PMCID: PMC415762 DOI: 10.1128/jb.186.11.3656-3659.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Butyrivibrio fibrisolvens tet(W) gene is located on the conjugative transposon TnB1230. TnB1230 encodes transfer proteins with 48 to 67% identity to some of those encoded by Tn1549. tet(W) is flanked by directly repeated sequences with significant homology to oxygen-insensitive nitroreductases. The 340 nucleotides upstream of tet(W) are strongly conserved and are required for tetracycline resistance.
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Affiliation(s)
- Claire M Melville
- Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, United Kingdom
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Blake DP, Humphry RW, Scott KP, Hillman K, Fenlon DR, Low JC. Influence of tetracycline exposure on tetracycline resistance and the carriage of tetracycline resistance genes within commensal Escherichia coli populations. J Appl Microbiol 2003; 94:1087-97. [PMID: 12752819 DOI: 10.1046/j.1365-2672.2003.01937.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To assess the influence of incremental tetracycline exposure on the genetic basis of tetracycline resistance within faecal Escherichia coli. METHODS AND RESULTS Through the adoption of a novel combination of multiple breakpoint selection, phenotypic characterization and the application of a polymerase chain reaction based gene identification system it proved possible to monitor the influence of antibiotic exposure on resistance gene possession. Using tetracycline as a case study a clear hierarchy was revealed between tet genes, strongly influenced by host antimicrobial exposure history. CONCLUSIONS The antimicrobial exposure regime under which an animal is produced affects both the identity and magnitude of resistance gene possession of a selected bacterial population within its enteric microflora. Among the ramifications associated with such resistance gene selection is the degree of resistance conferred and the carriage of linked resistance determinants. This selection is applied by exposure to antibiotic concentrations well below recognized minimum inhibitory tetracycline concentration breakpoints widely adopted to characterize bacterial 'susceptibility'. SIGNIFICANCE AND IMPACT OF THE STUDY This study confirms the ability of minimal antibiotic exposure to select for the continued persistence of resistance genes within the enteric microflora. It is clearly demonstrated that different antimicrobial regimes select for different resistance genes, the implications of which are discussed.
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Affiliation(s)
- D P Blake
- Centre for Microbiological Research, Veterinary Science Division, SAC, Craibstone, Aberdeen, UK.
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Devillard E, Bera-Maillet C, Flint HJ, Scott KP, Newbold CJ, Wallace RJ, Jouany JP, Forano E. Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydrate-binding module that binds to cellulose. Biochem J 2003; 373:495-503. [PMID: 12693992 PMCID: PMC1223500 DOI: 10.1042/bj20021784] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 04/04/2003] [Accepted: 04/14/2003] [Indexed: 11/17/2022]
Abstract
A new xylanase gene, xyn10B, was isolated from the ruminal protozoan Polyplastron multivesiculatum and the gene product was characterized. XYN10B is the first protozoan family 10 glycoside hydrolase characterized so far and is a modular enzyme comprising a family 22 carbohydrate-binding module (CBM) preceding the catalytic domain. The CBM22 was shown to be a true CBM. It showed high affinity for soluble arabinoxylan and is the first example of a CBM22 that binds strongly to celluloses of various crystallinities. The enzymic properties of XYN10B were also analysed. Its optimal temperature and pH for activity were 39 degrees C and 7.0 respectively; these values being close to those of the ruminal ecosystem. The phylogenetic relationships between the XYN10B CBM22 or catalytic domain and related sequences from ruminal and non-ruminal bacteria and eukaryotes are reported. The xyn10B gene is shown to lack introns.
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Affiliation(s)
- Estelle Devillard
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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Duncan SH, Scott KP, Ramsay AG, Harmsen HJM, Welling GW, Stewart CS, Flint HJ. Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system. Appl Environ Microbiol 2003; 69:1136-42. [PMID: 12571040 PMCID: PMC143671 DOI: 10.1128/aem.69.2.1136-1142.2003] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Duplicate anaerobic fermentor systems were used to examine changes in a community of human fecal bacteria supplied with different carbohydrate energy sources. A panel of group-specific fluorescent in situ hybridization probes targeting 16S rRNA sequences revealed that the fermentors supported growth of a greater proportion of Bacteroides and a lower proportion of gram-positive anaerobes related to Faecalibacterium prausnitzii, Ruminococcus flavefaciens-Ruminococcus bromii, Eubacterium rectale-Clostridium coccoides, and Eubacterium cylindroides than the proportions in the starting fecal inoculum. Nevertheless, certain substrates, such as dahlia inulin, caused a pronounced increase in the number of bacteria related to R. flavefaciens-R. bromii and E. cylindroides. The ability of three strictly anaerobic, gram-positive bacteria to compete with the complete human fecal flora was tested in the same experiment by using selective plating to enumerate the introduced strains. The Roseburia-related strain A2-183(F) was able to grow on all substrates despite the fact that it was unable to utilize complex carbohydrates in pure culture, and it was assumed that this organism survived by cross-feeding. In contrast, Roseburia intestinalis L1-82(R) and Eubacterium sp. strain A2-194(R) survived less well despite the fact that they were able to utilize polysaccharides in pure culture, except that A2-194(R) was stimulated 100-fold by inulin. These results suggest that many low-G+C-content gram-positive obligate anaerobes may be selected against during in vitro incubation, although several groups were stimulated by inulin. Thus, considerable caution is necessary when workers attempt to predict the in vivo effects of probiotics and prebiotics from their effects in vitro.
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Affiliation(s)
- Sylvia H Duncan
- Gut Microbiology and Immunology Division, Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, United Kingdom
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Abstract
There is huge potential for genetic exchange to occur within the dense, diverse anaerobic microbial population inhabiting the gastrointestinal tract (GIT) of humans and animals. However, the incidence of conjugative transposons (CTns) and the antibiotic resistance genes they carry has not been well studied among this population. Since any incoming bacteria, including pathogens, can access this reservoir of genes, this oversight would appear to be an important one. Recent evidence has shown that anaerobic bacteria native to the rumen or hindgut harbour both novel antibiotic resistance genes and novel conjugative transposons. These CTns, and previously characterized CTns, can be transferred to a wide range of commensal bacteria under laboratory and in vivo conditions. The main evidence that gene transfer occurs widely in vivo between GIT bacteria, and between GIT bacteria and pathogenic bacteria, is that identical resistance genes are present in diverse bacterial species from different hosts.
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Affiliation(s)
- K P Scott
- Gut Microbiology and Immunology Division, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, United Kingdom.
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Melville CM, Scott KP, Mercer DK, Flint HJ. Novel tetracycline resistance gene, tet(32), in the Clostridium-related human colonic anaerobe K10 and its transmission in vitro to the rumen anaerobe Butyrivibrio fibrisolvens. Antimicrob Agents Chemother 2001; 45:3246-9. [PMID: 11600392 PMCID: PMC90818 DOI: 10.1128/aac.45.11.3246-3249.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel tetracycline resistance gene, designated tet(32), which confers a high level of tetracycline resistance, was identified in the Clostridium-related human colonic anaerobe K10, which also carries tet(W). tet(32) was transmissible in vitro to the rumen anaerobe Butyrivibrio fibrisolvens 2221(R). The predicted gene product of tet(32) has 76% amino acid identity with Tet(O). PCR amplification indicated that tet(32) is widely distributed in the ovine rumen and in porcine feces.
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Affiliation(s)
- C M Melville
- Rowett Research Institute, Bucksburn, Aberdeen, United Kingdom AB21 9SB
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Rincón MT, McCrae SI, Kirby J, Scott KP, Flint HJ. EndB, a multidomain family 44 cellulase from Ruminococcus flavefaciens 17, binds to cellulose via a novel cellulose-binding module and to another R. flavefaciens protein via a dockerin domain. Appl Environ Microbiol 2001; 67:4426-31. [PMID: 11571138 PMCID: PMC93185 DOI: 10.1128/aem.67.10.4426-4431.2001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms by which cellulolytic enzymes and enzyme complexes in Ruminococcus spp. bind to cellulose are not fully understood. The product of the newly isolated cellulase gene endB from Ruminococcus flavefaciens 17 was purified as a His-tagged product after expression in Escherichia coli and found to be able to bind directly to crystalline cellulose. The ability to bind cellulose is shown to be associated with a novel cellulose-binding module (CBM) located within a region of 200 amino acids that is unrelated to known protein sequences. EndB (808 amino acids) also contains a catalytic domain belonging to glycoside hydrolase family 44 and a C-terminal dockerin-like domain. Purified EndB is also shown to bind specifically via its dockerin domain to a polypeptide of ca. 130 kDa present among supernatant proteins from Avicel-grown R. flavefaciens that attach to cellulose. The protein to which EndB attaches is a strong candidate for the scaffolding component of a cellulosome-like multienzyme complex recently identified in this species (S.-Y. Ding et al., J. Bacteriol. 183:1945-1953, 2001). It is concluded that binding of EndB to cellulose may occur both through its own CBM and potentially also through its involvement in a cellulosome complex.
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Affiliation(s)
- M T Rincón
- Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, United Kingdom
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49
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Mercer DK, Scott KP, Melville CM, Glover LA, Flint HJ. Transformation of an oral bacterium via chromosomal integration of free DNA in the presence of human saliva. FEMS Microbiol Lett 2001; 200:163-7. [PMID: 11425469 DOI: 10.1111/j.1574-6968.2001.tb10709.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Transformation of Streptococcus gordonii DL1 by free DNA was studied in human saliva. Competent S. gordonii could be transformed in vitro with plasmid DNA that had been taken into the human mouth. Transformation also occurred with a plasmid that cannot replicate in S. gordonii, but that has a region of chromosomal homology, by integration into the bacterial chromosome, although linearised plasmid DNA gave no transformants. Linear chromosomal DNA fragments did however transform S. gordonii/Tn916 efficiently in saliva when regions of homology with the recipient chromosome flanked the marker gene. These findings are discussed in relation to the potential for acquisition of DNA sequences, including genetically modified DNA, by gut and oral bacteria.
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Affiliation(s)
- D K Mercer
- Rowett Research Institute, Bucksburn, Aberdeen, UK.
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50
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Aurilia V, Martin JC, McCrae SI, Scott KP, Rincon MT, Flint HJ. Three multidomain esterases from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 that carry divergent dockerin sequences. Microbiology (Reading) 2000; 146 ( Pt 6):1391-1397. [PMID: 10846217 DOI: 10.1099/00221287-146-6-1391] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three enzymes carrying esterase domains have been identified in the rumen cellulolytic anaerobe Ruminococcus flavefaciens 17. The newly characterized CesA gene product (768 amino acids) includes an N-terminal acetylesterase domain and an unidentified C-terminal domain, while the previously characterized XynB enzyme (781 amino acids) includes an internal acetylesterase domain in addition to its N-terminal xylanase catalytic domain. A third gene, xynE, is predicted to encode a multidomain enzyme of 792 amino acids including a family 11 xylanase domain and a C-terminal esterase domain. The esterase domains from CesA and XynB share significant sequence identity (44%) and belong to carbohydrate esterase family 3; both domains are shown here to be capable of deacetylating acetylated xylans, but no evidence was found for ferulic acid esterase activity. The esterase domain of XynE, however, shares 42% amino acid identity with a family 1 phenolic acid esterase domain identified from Clostridum thermocellum XynZ. XynB, XynE and CesA all contain dockerin-like regions in addition to their catalytic domains, suggesting that these enzymes form part of a cellulosome-like multienzyme complex. The dockerin sequences of CesA and XynE differ significantly from those previously described in R. flavefaciens polysaccharidases, including XynB, suggesting that they might represent distinct dockerin specificities.
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Affiliation(s)
- Vincenzo Aurilia
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK1
| | - Jennifer C Martin
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK1
| | - Sheila I McCrae
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK1
| | - Karen P Scott
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK1
| | - Marco T Rincon
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK1
| | - Harry J Flint
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK1
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