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Gänzle MG, Monnin L, Zheng J, Zhang L, Coton M, Sicard D, Walter J. Starter Culture Development and Innovation for Novel Fermented Foods. Annu Rev Food Sci Technol 2024; 15:211-239. [PMID: 38052450 DOI: 10.1146/annurev-food-072023-034207] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Interest in fermented foods is increasing because fermented foods are promising solutions for more secure food systems with an increased proportion of minimally processed plant foods and a smaller environmental footprint. These developments also pertain to novel fermented food for which no traditional template exists, raising the question of how to develop starter cultures for such fermentations. This review establishes a framework that integrates traditional and scientific knowledge systems for the selection of suitable cultures. Safety considerations, the use of organisms in traditional food fermentations, and the link of phylogeny to metabolic properties provide criteria for culture selection. Such approaches can also select for microbial strains that have health benefits. A science-based approach to the development of novel fermented foods can substantially advance their value through more secure food systems, food products that provide health-promoting microbes, and the provision of foods that improve human health.
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Affiliation(s)
- Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada;
- College of Bioengineering and Food Science, Hubei University of Technology, Wuhan, Hubei, People's Republic of China
| | - Ludovic Monnin
- SPO, Université Montpellier, INRAE, Institut Agro, Montpellier, France
- Lallemand Oenology, Blagnac, France
| | - Jinshui Zheng
- National Key Laboratory for Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Lingxiao Zhang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada;
| | - Monika Coton
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université de Brest, INRAE, Plouzané, France
| | - Delphine Sicard
- SPO, Université Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
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2
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Gänzle MG, Qiao N, Bechtner J. The quest for the perfect loaf of sourdough bread continues: Novel developments for selection of sourdough starter cultures. Int J Food Microbiol 2023; 407:110421. [PMID: 37806010 DOI: 10.1016/j.ijfoodmicro.2023.110421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Sourdough fermentation, one of the oldest unit operations in food production, is currently experiencing a revival in bread production at the household, artisanal, and the industrial level. The expanding use of sourdough fermentation in bread production and the adaptation of fermentation to large scale industrial bread production also necessitate the development of novel starter cultures. Developments in the last years also have expanded the tools that are used to assess the metabolic potential of specific strains, species or genera of the Lactobacillaceae and have identified multiple ecological and metabolic traits as clade-specific. This review aims to provide an overview on the clade-specific metabolic potential of members of the Lactobacillaceae for use in sourdough baking, and the impact of these clade-specific traits on bread quality. Emphasis is placed on carbohydrate metabolism, including the conversion of sucrose and starch to soluble polysaccharides, conversion of amino acids, and the metabolism of organic acids. The current state of knowledge to compose multi-strain starter cultures (synthetic microbial communities) that are suitable for back-slopping will also be discussed. Taken together, the communication outlines the current tools for selection of microbes for use in sourdough baking.
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Affiliation(s)
- Michael G Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Canada.
| | - Nanzhen Qiao
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Canada
| | - Julia Bechtner
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Canada
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3
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Li X, Lin Y, Chen Y, Sui H, Chen J, Li J, Zhang G, Yan Y. The effects of race and probiotic supplementation on the intestinal microbiota of 10-km open-water swimmers. Heliyon 2023; 9:e22735. [PMID: 38144321 PMCID: PMC10746432 DOI: 10.1016/j.heliyon.2023.e22735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
This study collected the stools of 10-km open-water swimmers after race and probiotic supplementation, and 16S rRNA sequencing and metabolomic analysis were performed to clarify their intestinal microbiota characteristics. The findings revealed a relatively high proportion of Firmicutes in all the athletes. Firmicutes in female athletes were significantly higher after probiotic supplementation. The intestinal microbiota of athletes was closely associated with the pathways of exercise against cancer, exercise against aging, exercise for improving cognition, sphingolipid metabolism and endocrine resistance. Future research should focus on the relationship between Firmicutes and Proteobacteria with super class metabolites in athletes. This report initially explored the changes in intestinal microbiota involved in metabolic pathways in athletes after race and after probiotic supplementation and provided a theoretical basis for the further improvement of the monitoring of their physical function after race and selection of nutritional strategies during exercise training.
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Affiliation(s)
- Xuehan Li
- Sport Science School, Beijing Sport University, Beijing, China
| | - Yihsuan Lin
- Sport Science School, Beijing Sport University, Beijing, China
| | - Yue Chen
- Sport Science School, Beijing Sport University, Beijing, China
| | - Hongtao Sui
- Sport Science School, Beijing Sport University, Beijing, China
| | - Jianhao Chen
- Sport Science School, Beijing Sport University, Beijing, China
| | - Jiaqi Li
- Sport Science School, Beijing Sport University, Beijing, China
| | - Guoqing Zhang
- Shandong Swimming Sports Management Center, Shandong, China
| | - Yi Yan
- Sport Science School, Beijing Sport University, Beijing, China
- Key Laboratory of Exercise and Physical Fitness (Beijing Sport University), Ministry of Education, Beijing, China
- Laboratory of Sports Stress and Adaptation of General Administration of Sport, Beijing, China
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4
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Walter J, O'Toole PW. Microbe Profile: The Lactobacillaceae. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001414. [PMID: 38088348 PMCID: PMC10765037 DOI: 10.1099/mic.0.001414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023]
Abstract
The bacterial family Lactobacillaceae (the lactobacilli) occupy a unique role in microbiology due to their beneficial role in both human cultural history and biology, from the food preservation of hunter gatherers-turned-farmers, through the prevention of scurvy in seafarers exploring new worlds, and the health-promoting properties of species that colonize the human body as well as animals that are important for agriculture and pollination. The almost bewildering phenotypic and genomic complexity of the former genus Lactobacillus was recently reconciled with molecular taxonomy and phylogeny to establish robust genera comprising the Lactobacillaceae , whose main features are summarized in this Microbe Profile.
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Affiliation(s)
- Jens Walter
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
| | - Paul W. O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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5
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Lebeer S, Ahannach S, Gehrmann T, Wittouck S, Eilers T, Oerlemans E, Condori S, Dillen J, Spacova I, Vander Donck L, Masquillier C, Allonsius CN, Bron PA, Van Beeck W, De Backer C, Donders G, Verhoeven V. A citizen-science-enabled catalogue of the vaginal microbiome and associated factors. Nat Microbiol 2023; 8:2183-2195. [PMID: 37884815 PMCID: PMC10627828 DOI: 10.1038/s41564-023-01500-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/13/2023] [Indexed: 10/28/2023]
Abstract
Understanding the composition and function of the vaginal microbiome is crucial for reproductive and overall health. Here we established the Isala citizen-science project to analyse the vaginal microbiomes of 3,345 women in Belgium (18-98 years) through self-sampling, 16S amplicon sequencing and extensive questionnaires. The overall vaginal microbiome composition was strongly tied to age, childbirth and menstrual cycle phase. Lactobacillus species dominated 78% of the vaginal samples. Specific bacterial taxa also showed to co-occur in modules based on network correlation analysis. Notably, the module containing Lactobacillus crispatus, Lactobacillus jensenii and Limosilactobacillus taxa was positively linked to oestrogen levels and contraceptive use and negatively linked to childbirth and breastfeeding. Other modules, named after abundant taxa (Gardnerella, Prevotella and Bacteroides), correlated with multiple partners, menopause, menstrual hygiene and contraceptive use. With this resource-rich vaginal microbiome map and associated health, life-course, lifestyle and dietary factors, we provide unique data and insights for follow-up clinical and mechanistic research.
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Affiliation(s)
- Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium.
| | - Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Thies Gehrmann
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Tom Eilers
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Eline Oerlemans
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Sandra Condori
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Jelle Dillen
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Leonore Vander Donck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Caroline Masquillier
- Department of Sociology, Center for Population, Family and Health, University of Antwerp, Antwerp, Belgium
| | - Camille Nina Allonsius
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Peter A Bron
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Wannes Van Beeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | | | - Gilbert Donders
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium
- Regional Hospital Heilig Hart, Tienen, Belgium
- Femicare Clinical Research for Women, Tienen, Belgium
| | - Veronique Verhoeven
- Department of Family Medicine and Population Health, University of Antwerp, Antwerp, Belgium
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6
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Jie Z, Zhu Q, Zou Y, Wu Q, Qin M, He D, Lin X, Tong X, Zhang J, Jie Z, Luo W, Xiao X, Chen S, Wu Y, Guo G, Zheng S, Li Y, Lai W, Yang H, Wang J, Xiao L, Chen J, Zhang T, Kristiansen K, Jia H, Zhong S. A consortium of three-bacteria isolated from human feces inhibits formation of atherosclerotic deposits and lowers lipid levels in a mouse model. iScience 2023; 26:106960. [PMID: 37378328 PMCID: PMC10291474 DOI: 10.1016/j.isci.2023.106960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/21/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
By a survey of metagenome-wide association studies (MWAS), we found a robust depletion of Bacteroides cellulosilyticus, Faecalibacterium prausnitzii, and Roseburia intestinalis in individuals with atherosclerotic cardiovascular disease (ACVD). From an established collection of bacteria isolated from healthy Chinese individuals, we selected B. cellulosilyticus, R. intestinalis, and Faecalibacterium longum, a bacterium related to F. prausnitzii, and tested the effects of these bacteria in an Apoe/- atherosclerosis mouse model. We show that administration of these three bacterial species to Apoe-/- mice robustly improves cardiac function, reduces plasma lipid levels, and attenuates the formation of atherosclerotic plaques. Comprehensive analysis of gut microbiota, plasma metabolome, and liver transcriptome revealed that the beneficial effects are associated with a modulation of the gut microbiota linked to a 7α-dehydroxylation-lithocholic acid (LCA)-farnesoid X receptor (FXR) pathway. Our study provides insights into transcriptional and metabolic impact whereby specific bacteria may hold promises for prevention/treatment of ACVD.
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Affiliation(s)
- Zhuye Jie
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
| | - Qian Zhu
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- School of Medicine, South China University of Technology, Guangzhou 510006, P.R. China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Qili Wu
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- School of Medicine, South China University of Technology, Guangzhou 510006, P.R. China
| | - Min Qin
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- School of Medicine, South China University of Technology, Guangzhou 510006, P.R. China
| | | | | | | | | | - Zhu Jie
- BGI-Shenzhen, Shenzhen, China
| | - Wenwei Luo
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Xiao Xiao
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Shiyu Chen
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Yonglin Wu
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Gongjie Guo
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- School of Medicine, South China University of Technology, Guangzhou 510006, P.R. China
| | - Shufen Zheng
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Yong Li
- Department of Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Weihua Lai
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Jiyan Chen
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
| | - Tao Zhang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | - Shilong Zhong
- Department of Pharmacy, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, P.R. China
- School of Medicine, South China University of Technology, Guangzhou 510006, P.R. China
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7
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Li F, Li X, Cheng CC, Bujdoš D, Tollenaar S, Simpson DJ, Tasseva G, Perez-Muñoz ME, Frese S, Gänzle MG, Walter J, Zheng J. A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans. BMC Biol 2023; 21:53. [PMID: 36907868 PMCID: PMC10010030 DOI: 10.1186/s12915-023-01541-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Gut microbes play crucial roles in the development and health of their animal hosts. However, the evolutionary relationships of gut microbes with vertebrate hosts, and the consequences that arise for the ecology and lifestyle of the microbes are still insufficiently understood. Specifically, the mechanisms by which strain-level diversity evolved, the degree by which lineages remain stably associated with hosts, and how their evolutionary history influences their ecological performance remain a critical gap in our understanding of vertebrate-microbe symbiosis. RESULTS This study presents the characterization of an extended collection of strains of Limosilactobacillus reuteri and closely related species from a wide variety of hosts by phylogenomic and comparative genomic analyses combined with colonization experiments in mice to gain insight into the long-term evolutionary relationship of a bacterial symbiont with vertebrates. The phylogenetic analysis of L. reuteri revealed early-branching lineages that primarily consist of isolates from rodents (four lineages) and birds (one lineage), while lineages dominated by strains from herbivores, humans, pigs, and primates arose more recently and were less host specific. Strains from rodent lineages, despite their phylogenetic divergence, showed tight clustering in gene-content-based analyses. These L. reuteri strains but not those ones from non-rodent lineages efficiently colonize the forestomach epithelium of germ-free mice. The findings support a long-term evolutionary relationships of L. reuteri lineages with rodents and a stable host switch to birds. Associations of L. reuteri with other host species are likely more dynamic and transient. Interestingly, human isolates of L. reuteri cluster phylogenetically closely with strains from domesticated animals, such as chickens and herbivores, suggesting zoonotic transmissions. CONCLUSIONS Overall, this study demonstrates that the evolutionary relationship of a vertebrate gut symbiont can be stable in particular hosts over time scales that allow major adaptations and specialization, but also emphasizes the diversity of symbiont lifestyles even within a single bacterial species. For L. reuteri, symbiont lifestyles ranged from autochthonous, likely based on vertical transmission and stably aligned to rodents and birds over evolutionary time, to allochthonous possibly reliant on zoonotic transmission in humans. Such information contributes to our ability to use these microbes in microbial-based therapeutics.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Christopher C Cheng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Dalimil Bujdoš
- School of Microbiology, and Department of Medicine, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Stephanie Tollenaar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - David J Simpson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Guergana Tasseva
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Steven Frese
- Department of Nutrition, University of Nevada, Reno, NV, 89557, USA
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,School of Microbiology, and Department of Medicine, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China.
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8
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Zhang Z, Guo Q, Wang J, Tan H, Jin X, Fan Y, Liu J, Zhao S, Zheng J, Peng N. Postbiotics from Pichia kudriavzevii promote intestinal health performance through regulation of Limosilactobacillus reuteri in weaned piglets. Food Funct 2023; 14:3463-3474. [PMID: 36912248 DOI: 10.1039/d2fo03695a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Postbiotics are attractive as alternatives to antibiotics for use against post-weaning diarrhea. However, their beneficial mechanisms are largely unknown. In the current study, we first demonstrated that supplementation with 0.5% Pichia kudriavzevii FZ12 postbiotics in the diet significantly reduced diarrhea incidence, promoted growth performance, improved gut health performance, and significantly enriched beneficial bacteria, particularly Lactobacillus spp., in the intestines of weaned piglets. Importantly, we identified a heat- and proteinase K-sensitive component, cytochrome c, of the postbiotics that significantly promoted the growth and biofilm formation of Limosilactobacillus reuteri FP13. We demonstrated the importance of P. kudriavzevii FZ12 postbiotics in improving the intestinal health of a model animal and revealed that cytochrome c is one of the important components of yeast postbiotics. These findings may provide new insights into microbe-postbiotics interplay that can be applied to guidelines for dietary modulation to alleviate weaning-induced diarrhea.
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Affiliation(s)
- Zhenting Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China. .,The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, P.R. China
| | - Qiujin Guo
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Jing Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Hongyan Tan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Xuexia Jin
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Yurong Fan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Jiali Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
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9
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Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
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Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
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10
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Petitfils C, Maurel S, Payros G, Hueber A, Agaiz B, Gazzo G, Marrocco R, Auvray F, Langevin G, Motta JP, Floch P, Tremblay-Franco M, Galano JM, Guy A, Durand T, Lachambre S, Durbec A, Hussein H, Decraecker L, Bertrand-Michel J, Saoudi A, Oswald E, Poisbeau P, Dietrich G, Melchior C, Boeckxstaens G, Serino M, Le Faouder P, Cenac N. Identification of bacterial lipopeptides as key players in IBS. Gut 2022; 72:939-950. [PMID: 36241390 PMCID: PMC10086498 DOI: 10.1136/gutjnl-2022-328084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/27/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVES Clinical studies revealed that early-life adverse events contribute to the development of IBS in adulthood. The aim of our study was to investigate the relationship between prenatal stress (PS), gut microbiota and visceral hypersensitivity with a focus on bacterial lipopeptides containing γ-aminobutyric acid (GABA). DESIGN We developed a model of PS in mice and evaluated, in adult offspring, visceral hypersensitivity to colorectal distension (CRD), colon inflammation, barrier function and gut microbiota taxonomy. We quantified the production of lipopeptides containing GABA by mass spectrometry in a specific strain of bacteria decreased in PS, in PS mouse colons, and in faeces of patients with IBS and healthy volunteers (HVs). Finally, we assessed their effect on PS-induced visceral hypersensitivity. RESULTS Prenatally stressed mice of both sexes presented visceral hypersensitivity, no overt colon inflammation or barrier dysfunction but a gut microbiota dysbiosis. The dysbiosis was distinguished by a decreased abundance of Ligilactobacillus murinus, in both sexes, inversely correlated with visceral hypersensitivity to CRD in mice. An isolate from this bacterial species produced several lipopeptides containing GABA including C14AsnGABA. Interestingly, intracolonic treatment with C14AsnGABA decreased the visceral sensitivity of PS mice to CRD. The concentration of C16LeuGABA, a lipopeptide which inhibited sensory neurons activation, was decreased in faeces of patients with IBS compared with HVs. CONCLUSION PS impacts the gut microbiota composition and metabolic function in adulthood. The reduced capacity of the gut microbiota to produce GABA lipopeptides could be one of the mechanisms linking PS and visceral hypersensitivity in adulthood.
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Affiliation(s)
- Camille Petitfils
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Sarah Maurel
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Gaelle Payros
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Amandine Hueber
- Lipidomic, MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Bahija Agaiz
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Géraldine Gazzo
- Institut des Neurosciences Cellulaire et Integrative (INCI), Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Rémi Marrocco
- INFINITY, Université de Toulouse-Paul Sabatier, INSERM, CNRS, UPS, Toulouse, France
| | - Frédéric Auvray
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Geoffrey Langevin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Jean-Paul Motta
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Pauline Floch
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France.,Service de bactériologie-hygiène, CHU Toulouse, Hôpital Purpan, Toulouse, France
| | - Marie Tremblay-Franco
- Toxalim (Research Center in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.,Metatoul-AXIOM Platform, MetaboHUB, Toxalim, INRAE, Toulouse, France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Alexandre Guy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Simon Lachambre
- INFINITY, Université de Toulouse-Paul Sabatier, INSERM, CNRS, UPS, Toulouse, France
| | - Anaëlle Durbec
- Lipidomic, MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Hind Hussein
- Laboratory of Intestinal Neuro-immune Interaction, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Lisse Decraecker
- Laboratory of Intestinal Neuro-immune Interaction, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Justine Bertrand-Michel
- Lipidomic, MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Abdelhadi Saoudi
- INFINITY, Université de Toulouse-Paul Sabatier, INSERM, CNRS, UPS, Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France.,Service de bactériologie-hygiène, CHU Toulouse, Hôpital Purpan, Toulouse, France
| | - Pierrick Poisbeau
- Institut des Neurosciences Cellulaire et Integrative (INCI), Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Gilles Dietrich
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Chloe Melchior
- Gastroenterology Department, Rouen University Hospital, Rouen, France.,Institute for Research and Innovation in Biomedicine, INSERM CIC-CRB 1404, INSERM UMR 1073, Normandy University, Rouen, France.,Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Guy Boeckxstaens
- Laboratory of Intestinal Neuro-immune Interaction, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Matteo Serino
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Pauline Le Faouder
- Lipidomic, MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,I2MC, Université de Toulouse, Inserm, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Nicolas Cenac
- IRSD, Université de Toulouse-Paul Sabatier, INSERM, INRAe, ENVT, UPS, Toulouse, France
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11
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Gao J, Sadiq FA, Zheng Y, Zhao J, He G, Sang Y. Biofilm-based delivery approaches and specific enrichment strategies of probiotics in the human gut. Gut Microbes 2022; 14:2126274. [PMID: 36175161 PMCID: PMC9542427 DOI: 10.1080/19490976.2022.2126274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The use of probiotics has been one of the effective strategies to restructure perturbed human gut microbiota following a disease or metabolic disorder. One of the biggest challenges associated with the use of probiotic-based gut modulation strategies is to keep the probiotic cells viable and stable during the gastrointestinal transit. Biofilm-based probiotics delivery approaches have emerged as fascinating modes of probiotic delivery in which probiotics show significantly greater tolerance and biotherapeutic potential, and interestingly probiotic biofilms can be developed on food-grade surfaces too, which is ideal for the growth and proliferation of bacterial cells for incorporation into food matrices. In addition, biofilms can be further encapsulated with food-grade materials or with bacterial self-produced biofilms. This review presents a newly emerging and unprecedently discussed techniques for the safe delivery of probiotics based on biofilms and further discusses newly emerging prebiotic materials which target specific gut microbiota groups for growth and proliferation.
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Affiliation(s)
- Jie Gao
- Collge of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Faizan Ahmed Sadiq
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Yixin Zheng
- Collge of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Jinrong Zhao
- Collge of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Guoqing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China,CONTACT Guoqing He College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Yaxin Sang
- Collge of Food Science and Technology, Hebei Agricultural University, Baoding, China,Yaxin Sang Collge of Food Science and Technology, Hebei Agricultural University, Baoding, China
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12
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Özçam M, Oh JH, Tocmo R, Acharya D, Zhang S, Astmann TJ, Heggen M, Ruiz-Ramírez S, Li F, Cheng CC, Vivas E, Rey FE, Claesen J, Bugni TS, Walter J, van Pijkeren JP. A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation. Cell Host Microbe 2022; 30:824-835.e6. [PMID: 35443156 DOI: 10.1016/j.chom.2022.03.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/16/2021] [Accepted: 03/25/2022] [Indexed: 11/03/2022]
Abstract
The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters; yet, their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun, cluster encodes antimicrobial activity. Forty-one of 51 L. reuteri strains tested are sensitive to Pks products; this finding was independent of strains' host origin. Sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and -sensitive strains identified an acyltransferase gene (act) unique to Pks-resistant strains. Subsequent cell-wall analysis of wild-type and act mutant strains showed that Act acetylates cell-wall components, providing resistance to Pks-mediated killing. Additionally, pks mutants lost their competitive advantage, while act mutants lost their Pks resistance in in vivo competition assays. These findings provide insight into how closely related gut symbionts can compete and co-exist in the gastrointestinal tract.
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Affiliation(s)
- Mustafa Özçam
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Restituto Tocmo
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Deepa Acharya
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Shenwei Zhang
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Theresa J Astmann
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark Heggen
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Christopher C Cheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Eugenio Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jan Claesen
- Department of Cardiovascular and Metabolic Sciences and Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada; Department of Medicine and APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland; School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Jan-Peter van Pijkeren
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA; Food Research Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Qiao N, Wittouck S, Mattarelli P, Zheng J, Lebeer S, Felis GE, Gänzle MG. After the storm-Perspectives on the taxonomy of Lactobacillaceae. JDS COMMUNICATIONS 2022; 3:222-227. [PMID: 36338818 PMCID: PMC9623751 DOI: 10.3168/jdsc.2021-0183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/18/2022] [Indexed: 04/23/2023]
Abstract
In 2020, a taxonomic reorganization of the lactic acid bacteria reclassified over 300 species in 7 genera and 2 families into one family, the Lactobacillaceae, with 31 genera including 23 new genera to include organisms formerly classified as Lactobacillus species. This communication aims to provide a debrief on the taxonomic reorganization of lactobacilli to identify shortcomings in the proposed taxonomic framework, and to outline perspectives and opportunities provided by the current taxonomy of the Lactobacillaceae. The current taxonomy of lactobacilli not only necessitates becoming familiar with 23 new genus names but also provides substantial new opportunities in scientific discovery and regulatory approval of these organisms. First, description of new species in the Lactobacillaceae is facilitated and a solid framework for description of novel genera is provided. Second, the current taxonomy greatly enhances the resolution of genus-level sequencing approaches (e.g., 16S rRNA-based metagenomics) when identifying the composition and function of microbial communities. Third, the current taxonomy greatly facilitates the formulation of hypotheses linking phylogeny to metabolism and ecology of lactobacilli.
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Affiliation(s)
- Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada T6G 2P5
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Giovanna E. Felis
- Department of Biotechnology, Verona University Culture Collection, University of Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada T6G 2P5
- Corresponding author:
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14
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Vazquez-Munoz R, Dongari-Bagtzoglou A. Anticandidal Activities by Lactobacillus Species: An Update on Mechanisms of Action. FRONTIERS IN ORAL HEALTH 2021; 2:689382. [PMID: 35048033 PMCID: PMC8757823 DOI: 10.3389/froh.2021.689382] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 12/15/2022] Open
Abstract
Lactobacilli are among the most studied bacteria in the microbiome of the orodigestive and genitourinary tracts. As probiotics, lactobacilli may provide various benefits to the host. These benefits include regulating the composition of the resident microbiota, preventing - or even potentially reverting- a dysbiotic state. Candida albicans is an opportunistic pathogen that can influence and be influenced by other members of the mucosal microbiota and, under immune-compromising conditions, can cause disease. Lactobacillus and Candida species can colonize the same mucosal sites; however, certain Lactobacillus species display antifungal activities that can contribute to low Candida burdens and prevent fungal infection. Lactobacilli can produce metabolites with direct anticandidal function or enhance the host defense mechanisms against fungi. Most of the Lactobacillus spp. anticandidal mechanisms of action remain underexplored. This work aims to comprehensively review and provide an update on the current knowledge regarding these anticandidal mechanisms.
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Affiliation(s)
- Roberto Vazquez-Munoz
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT, United States
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT, United States
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15
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Li XY, Li LX, Li Y, Zhou RC, Li B, Gu X, Fu SC, Jin BY, Zuo XL, Li YQ. Complete genome sequencing of Peyer's patches-derived Lactobacillus taiwanensis CLG01, a potential probiotic with antibacterial and immunomodulatory activity. BMC Microbiol 2021; 21:68. [PMID: 33639835 PMCID: PMC7916312 DOI: 10.1186/s12866-021-02127-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background The genus Lactobacillus is an important component of the gastrointestinal tract of human and animals and commonly considered as probiotic. L. taiwanensis has long been proposed to be a probiotic whereas understanding on this species is still in its infancy. Genomic information of L. taiwanensis is fairly limited. Extensive characterization of its beneficial traits is needed. Results A new strain CLG01 of L. taiwanensis was isolated from mouse Peyer’s patches. We established its probiotic profile through in vitro experiments. Complete genome of this strain was also sequenced and analyzed. L. taiwanensis CLG01 showed robust tolerance to acid and a degree of tolerance to bile salt with a promising antibacterial activity against a broad spectrum of pathogenic bacteria. In vitro treatment of mouse RAW 264.7 macrophage cells with heat-killed bacteria and bacterial supernatant of L. taiwanensis CLG01 resulted in enhancement of immune responses and upregulated expression of TNF-α and IL-6. The strain CLG01 also increased the IL-10 production of macrophages when co-treated with lipopolysaccharide (LPS). Complete genome of L. taiwanensis CLG01 contained a 1.89 Mb chromosome and two plasmids. Further genomic analysis revealed the presence of genes related to its resistance to different stresses and the beneficial effects mentioned above. Moreover, biosynthetic gene clusters (BGCs) encoding antimicrobial peptides, like bacteriocin, linear azol(in)e-containing peptide (LAP) and lanthipeptide, were also identified in the genome of L. taiwanensis CLG01. Conclusions L. taiwanensis CLG01, isolated from mouse Peyer’s patches, is the first L. taiwanensis strain with both phenotypes and genotypes systematically studied. These preliminary data confirmed the role of L. taiwanensis CLG01 as a potential probiotic candidate with antibacterial and immunomodulatory activity, which provide insight for further investigation to this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02127-z.
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Affiliation(s)
- Xiao-Yu Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Li-Xiang Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yan Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ru-Chen Zhou
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bing Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiang Gu
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shi-Chen Fu
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bi-Ying Jin
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiu-Li Zuo
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yan-Qing Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China. .,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China. .,Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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16
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Li F, Cheng CC, Zheng J, Liu J, Quevedo RM, Li J, Roos S, Gänzle MG, Walter J. Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts. Int J Syst Evol Microbiol 2021; 71:004644. [PMID: 33533708 PMCID: PMC8346765 DOI: 10.1099/ijsem.0.004644] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/20/2020] [Indexed: 01/17/2023] Open
Abstract
Ten strains, BG-AF3-AT, pH52_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB_1_1, STM3_1T, STM2_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri. However, average nucleotide identity and digital DNA-DNA hybridization values based on whole genomes were below 95 and 70 %, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacillus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspecies. Here we propose six subspecies of L. reuteri: L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Christopher C. Cheng
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, 430070, PR China
| | - Junhong Liu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Rodrigo Margain Quevedo
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Junjie Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, T12 YT20, Ireland
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17
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Han C, Song J, Hu J, Fu H, Feng Y, Mu R, Xing Z, Wang Z, Wang L, Zhang J, Wang C, Dong L. Smectite promotes probiotic biofilm formation in the gut for cancer immunotherapy. Cell Rep 2021; 34:108706. [PMID: 33567279 DOI: 10.1016/j.celrep.2021.108706] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 11/12/2020] [Accepted: 01/08/2021] [Indexed: 12/17/2022] Open
Abstract
Administration of probiotics to regulate the immune system is a potential anti-tumor strategy. However, oral administration of probiotics is ineffective because of the poor inhabitation of exogenous bacteria in host intestines. Here we report that smectite, a type of mineral clay and established anti-diarrhea drug, promotes expansion of probiotics (especially Lactobacillus) in the murine gut and subsequently elicits anti-tumor immune responses. The ion-exchangeable microstructure of smectite preferentially promotes lactic acid bacteria (LABs) to form biofilms on smectite in vitro and in vivo. In mouse models, smectite laden with LAB biofilms (Lactobacillus and Bifidobacterium) inhibits tumor growth (when used alone) and enhances the efficacy of chemotherapy or immunotherapy (when used in combination with either of them) by activating dendritic cells (DCs) via Toll-like receptor 2 (TLR2) signaling. Our findings suggest oral administration of smectite as a promising strategy to enrich probiotics in vivo for cancer immunotherapy.
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Affiliation(s)
- Congwei Han
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinji Song
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Junqing Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Huijie Fu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yanxian Feng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR
| | - Ruoyu Mu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR
| | - Zhen Xing
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhenzhen Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR; Medical School of Nanjing University, Nanjing, Jiangsu 21093, China
| | - Lintao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China; Medical School of Nanjing University, Nanjing, Jiangsu 21093, China.
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR.
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China; Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, Jiangsu 210023, China.
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18
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Zhang Z, Wang K, Oh JH, Zhang S, van Pijkeren JP, Cheng CC, Ren D, Wei H, Gänzle MG, Walter J. A Phylogenetic View on the Role of Glycerol for Growth Enhancement and Reuterin Formation in Limosilactobacillus reuteri. Front Microbiol 2021; 11:601422. [PMID: 33408707 PMCID: PMC7779471 DOI: 10.3389/fmicb.2020.601422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
Lineages within the species Limosilactobacillus reuteri have specialized to various hosts and their genomes reflect these adaptations. The pdu-cbi-cob-hem gene cluster is conserved in most human and poultry isolates but is infrequent in rodent and porcine isolates. This gene cluster confers the transformation of glycerol into 3-hydroxy-propionaldehyde (reuterin), which can either be secreted and function as precursor of the antimicrobial compound acrolein or serve as an electron acceptor that enhances the organisms’ growth rate. However, it remains unclear which of these two functions is more relevant for L. reuteri evolution and ecology. Here we characterized the effect of glycerol on growth rate and reuterin formation in L. reuteri strains across different phylogenetic lineages during growth on ecologically relevant carbohydrates. We further evaluated the innate reuterin resistance among these strains to infer a possible role of reuterin in the evolution of strains. Results revealed that the poultry/human lineage VI strain, L. reuteri DSM 17938 shows more growth enhancement through glycerol and greater capacity for reuterin production on glucose and maltose as compared to human lineage II strains. Interestingly, reuterin production in lineage II strains was significantly elevated on raffinose and lactose, reaching levels similar to DSM 17938. On all carbohydrates tested, reuterin production occurred during the exponential growth phase and became undetectable during the stationary growth phase. The amount of reuterin produced was sufficient to inhibit E. coli, suggesting that it could be ecologically relevant, but the resistance towards reuterin among L. reuteri strains was highly variable and, for the most part, unrelated to the strain’s capacity for reuterin production. Overall, the findings suggest differences in the substrate-specific regulation of the pdu cluster in L. reuteri lineages that might be reflective of their ecological niches, e.g., chicken foregut versus human infant and adult large intestine. Such information can inform future studies on the ecology of L. reuteri and guide the development of synbiotic applications to improve the therapeutic use of this species.
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Affiliation(s)
- Zhihong Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Kaiming Wang
- Department of Physiology, CEGIIR, University of Alberta, Edmonton, AB, Canada
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Shenwei Zhang
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Christopher C Cheng
- Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Dayong Ren
- Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Hua Wei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Michael G Gänzle
- Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jens Walter
- Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Department of Physiology, CEGIIR, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland.,Department of Medicine, University College Cork, Cork, Ireland
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19
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Mathis KA, Bronstein JL. Our Current Understanding of Commensalism. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-040844] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Commensalisms, interactions between two species in which one species benefits and the other experiences no net effect, are frequently mentioned in the ecological literature but are surprisingly little studied. Here we review and synthesize our limited understanding of commensalism. We then argue that commensalism is not a single type of interaction; rather, it is a suite of phenomena associated with distinct ecological processes and evolutionary consequences. For each form of commensalism we define, we present evidence for how, where, and why it occurs, including when it is evolutionarily persistent and when it is an occasional outcome of interactions that are usually mutualistic or antagonistic. We argue that commensalism should be of great interest in the study of species interactions due to its location at the center of the continuum between positive and negative outcomes. Finally, we offer a roadmap for future research.
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Affiliation(s)
- Kaitlyn A. Mathis
- Department of Biology, Clark University, Worcester, Massachusetts 01610, USA
| | - Judith L. Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
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20
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Milovic A, Bassam K, Shao H, Chatzistamou I, Tufts DM, Diuk-Wasser M, Barbour AG. Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America. PLoS One 2020; 15:e0231801. [PMID: 32817657 PMCID: PMC7446861 DOI: 10.1371/journal.pone.0231801] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/15/2020] [Indexed: 11/19/2022] Open
Abstract
The cricetine rodent Peromyscus leucopus is an important reservoir for several human zoonoses, including Lyme disease, in North America. Akin to hamsters, the white-footed deermouse has been unevenly characterized in comparison to the murid Mus musculus. To further understanding of P. leucopus' total genomic content, we investigated gut microbiomes of an outbred colony of P. leucopus, inbred M. musculus, and a natural population of P. leucopus. Metagenome and whole genome sequencing were combined with microbiology and microscopy approaches. A focus was the genus Lactobacillus, four diverse species of which were isolated from forestomach and feces of colony P. leucopus. Three of the species-L. animalis, L. reuteri, and provisionally-named species "L. peromysci"-were identified in fecal metagenomes of wild P. leucopus but not discernibly in samples from M. musculus. L. johnsonii, the fourth species, was common in M. musculus but absent or sparse in wild P. leucopus. Also identified in both colony and natural populations were a Helicobacter sp. in feces but not stomach, and a Tritrichomonas sp. protozoan in cecum or feces. The gut metagenomes of colony P. leucopus were similar to those of colony M. musculus at the family or higher level and for major subsystems. But there were multiple differences between species and sexes within each species in their gut metagenomes at orthologous gene level. These findings provide a foundation for hypothesis-testing of functions of individual microbial species and for interventions, such as bait vaccines based on an autochthonous bacterium and targeting P. leucopus for transmission-blocking.
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Affiliation(s)
- Ana Milovic
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Khalil Bassam
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hanjuan Shao
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina, United States of America
| | - Danielle M. Tufts
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, United States of America
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, United States of America
| | - Alan G. Barbour
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
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21
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Li Q, Loponen J, Gänzle MG. Characterization of the Extracellular Fructanase FruA in Lactobacillus crispatus and Its Contribution to Fructan Hydrolysis in Breadmaking. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8637-8647. [PMID: 32687341 DOI: 10.1021/acs.jafc.0c02313] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) trigger symptoms of irritable bowel syndrome (IBS). Fructan degradation during bread making reduces FODMAPs in bread while maintaining the content of dietary fiber. This study explored the presence of the fructanases FruA in lactobacilli and characterized its use in bread making. FruA was exclusively present in vertebrate-adapted lactobacilli. In Lactobacillus crispatus DSM29598, FruA was located in cell wall fractions and includes a SLAP domain. FruA hydrolyzed levan or inulin; expression of fruA was not subject to catabolite repression. Fructans in bread were reduced by less than 50% in a straight dough process; conventional sourdough fermentation reduced fructans in bread by 65-70%. Sourdough fermentation with L. crispatus reduced fructans in bread by more than 90%. In conclusion, reduction of FODMAP by sourdough fermentation may improve tolerance in many IBS patients. Fermentation with FruA-expressing L. crispatus DSM29598 produces a low FODMAP bread.
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Affiliation(s)
- Qing Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | | | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
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22
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Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1498] [Impact Index Per Article: 374.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
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Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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23
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Genetic Determinants of Hydroxycinnamic Acid Metabolism in Heterofermentative Lactobacilli. Appl Environ Microbiol 2020; 86:AEM.02461-19. [PMID: 31862715 DOI: 10.1128/aem.02461-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Phenolic acids are among the most abundant phenolic compounds in edible parts of plants. Lactic acid bacteria (LAB) metabolize phenolic acids, but the enzyme responsible for reducing hydroxycinnamic acids to phenylpropionic acids (HcrB) was only recently characterized in Lactobacillus plantarum In this study, heterofermentative LAB species were screened for their hydroxycinnamic acid metabolism. Data on strain-specific metabolism in combination with comparative genomic analyses identified homologs of HcrB as putative phenolic acid reductases. Par1 and HcrF both encode putative multidomain proteins with 25% and 63% amino acid identity to HcrB, respectively. Of these genes, par1 in L. rossiae and hcrF in L. fermentum were overexpressed in response to hydroxycinnamic acids. The deletion of par1 in L. rossiae led to the loss of phenolic acid metabolism. The strain-specific metabolism of phenolic acids was congruent with the genotype of lactobacilli; however, phenolic acid reductases were not identified in strains of Weissella cibaria that reduced hydroxycinnamic acids to phenylpropionic acids. Phylogenetic analysis of major genes involved in hydroxycinnamic acid metabolism in strains of the genus Lactobacillus revealed that Par1 was found to be the most widely distributed phenolic acid reductase, while HcrB was the least abundant, present in less than 9% of Lactobacillus spp. In conclusion, this study increased the knowledge on the genetic determinants of hydroxycinnamic acid metabolism, explaining the species- and strain-specific metabolic variations in lactobacilli and providing evidence of additional enzymes involved in hydroxycinnamic acid metabolism of lactobacilli.IMPORTANCE The metabolism of secondary plant metabolites, including phenolic compounds, by food-fermenting lactobacilli is a significant contributor to the safety, quality, and nutritional quality of fermented foods. The enzymes mediating hydrolysis, reduction, and decarboxylation of phenolic acid esters and phenolic acids in lactobacilli, however, are not fully characterized. The genomic analyses presented here provide evidence for three novel putative phenolic acid reductases. Matching comparative genomic analyses with phenotypic analysis and quantification of gene expression indicates that two of the three putative phenolic acid reductases, Par1 and HcrF, are involved in reduction of hydroxycinnamic acids to phenylpropionic acids; however, the activity of Par2 may be unrelated to phenolic acids and recognizes other secondary plant metabolites. These findings expand our knowledge on the metabolic potential of lactobacilli and facilitate future studies on activity and substrate specificity of enzymes involved in metabolism of phenolic compounds.
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24
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Sgobba E, Wendisch VF. Synthetic microbial consortia for small molecule production. Curr Opin Biotechnol 2019; 62:72-79. [PMID: 31627138 DOI: 10.1016/j.copbio.2019.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 11/26/2022]
Abstract
Microbial consortia were designed for the production of small molecules with 'labor' being divided between two or more microorganisms. Examples of linear designs are substrate conversion preceding target molecule production or subdivision of two consecutive steps of target molecule production. Here, we review synthetic biology design approaches for microbial consortia based on ecological principles and microbial interactions that is, mutualism, and commensalism. Besides highlighting the technical challenges regarding industrial application of synthetic microbial consortia, we forecast the extension of the concept from binary linear to ternary linear and more complex microbial consortia in biotechnological applications. Microbial consortia are here reviewed and proposed as a rational solution toward feedstock accessibility as it has been shown for production of l-lysine, l-pipecolic acid and cadaverine from starch or production of fumarate from microcrystalline cellulose and alkaline pre-treated corn, or alternatively to establish new multi-step pathway for the production of rosmarinic acid from xylose and glucose.
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Affiliation(s)
- Elvira Sgobba
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University Bielefeld, Germany.
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25
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Li Q, Tao Q, Teixeira JS, Shu-Wei Su M, Gänzle MG. Contribution of glutaminases to glutamine metabolism and acid resistance in Lactobacillus reuteri and other vertebrate host adapted lactobacilli. Food Microbiol 2019; 86:103343. [PMID: 31703887 DOI: 10.1016/j.fm.2019.103343] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 01/13/2023]
Abstract
The bacterial conversion of glutamine to glutamate is catalyzed by glutamine-amidotransferases or glutaminases. Glutamine deamination contributes to the formation of the bioactive metabolites glutamate, γ-aminobutyrate (GABA) and γ-glutamyl peptides, and to acid resistance. This study aimed to investigate the distribution of glutaminase(s) in lactobacilli, and to evaluate their contribution in L. reuteri to amino acid metabolism and acid resistance. Phylogenetic analysis of the glutaminases gls1, gls2 and gls3 in the genus Lactobacillus demonstrated that glutaminase is exclusively present in host-adapted species of lactobacilli. The disruption gls1, gls2 and gls3 in L. reuteri 100-23 had only a limited effect on the conversion of glutamine to glutamate, GABA, or γ-glutamyl peptides in sourdough. The disruption of all glutaminases in L. reuteri 100-23Δgls1Δgls2Δgls3 but not disruption of gls2 and gls3 eliminated the protective effect of glutamine on the survival of the strain at pH 2.5. Glutamine also enhanced acid resistance of L. reuteri 100-23ΔgadB and L. taiwanensis 107q, strains without glutamate decarboxylase activity. Taken together, the study demonstrates that glutaminases of lactobacilli do not contribute substantially to glutamine metabolism but enhance acid resistance. Their exclusive presence in host-adapted lactobacilli provides an additional link between the adaptation of lactobacilli to specific habitats and their functionality when used as probiotics and starter cultures.
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Affiliation(s)
- Qing Li
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada
| | - QianYing Tao
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada
| | - Jaunana S Teixeira
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada
| | - Marcia Shu-Wei Su
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada
| | - Michael G Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, Alberta, Canada; Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.
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26
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Liu R, Chen Y, Tian Z, Mao Z, Cheng H, Zhou H, Wang W. Enhancing microbial community performance on acid resistance by modified adaptive laboratory evolution. BIORESOURCE TECHNOLOGY 2019; 287:121416. [PMID: 31103940 DOI: 10.1016/j.biortech.2019.121416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 05/09/2023]
Abstract
A new strategy of three-step adaptive laboratory evolution (ALE) was developed to enhance the bioleaching performance of moderately thermophilic consortia. Through consortium construction, directed evolution and chemostat selection, an improved consortium (ALEend) that composed of Leptospirillum ferriphilum (80.32%), Sulfobacillus thermosulfidooxidans (15.82%) and Ferroplasma thermophilum (3.86%) was obtained, showing ferrous iron oxidation rate of 500 mgL-1h-1 and biomass production of 2.0 × 108 cells/mL at pH 0.75. During batch culturing, the ALEend consortium exhibited stable ferrous iron oxidation in wider conditions. PCA indicated that the communities were similar under fluctuating culture conditions, which demonstrated the stable community structure and the reinforced synergistic interactions resulting in the enhanced community performance. Pyrite bioleaching conducted at pH 1.5 and 0.75 revealed that the ALEend consortium extracted 26% and 55% more total iron relative to the original consortium. These findings indicated that the modified ALE may be a promising strategy for microbial community modification to enhance bioleaching.
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Affiliation(s)
- Ronghui Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yanzhi Chen
- South China Institute of Environmental Sciences, Guangzhou, China
| | - Zhuang Tian
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhenghua Mao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
| | - Wei Wang
- South China Institute of Environmental Sciences, Guangzhou, China
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27
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Olsen NMC, Røder HL, Russel J, Madsen JS, Sørensen SJ, Burmølle M. Priority of Early Colonizers but No Effect on Cohabitants in a Synergistic Biofilm Community. Front Microbiol 2019; 10:1949. [PMID: 31507562 PMCID: PMC6716445 DOI: 10.3389/fmicb.2019.01949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/08/2019] [Indexed: 12/20/2022] Open
Abstract
The arrival order of different species to a habitat can strongly impact community assembly and succession dynamics, thus influencing functionality. In this study, we asked how prior colonization of one community member would influence the assembly of a synergistic multispecies biofilm community grown in vitro. We expected that the prior arrival would confer an advantage, in particular for good biofilm formers. Yet, we did not know if the cohabitants would be impaired or benefit from the pre-colonization of one member, depending on its ability to form biofilm. We used a consortium consisting of four soil bacteria; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. This consortium has been shown to act synergistically when grown together, thus increasing biofilm production. The results showed that the two good biofilm formers gained a fitness advantage (increase in abundance) when allowed prior colonization on an abiotic surface before the arrival of their cohabitants. Interestingly, the significantly higher number of the pre-colonized biofilm formers did not affect the resulting composition in the subsequent biofilm after 24 h.
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Affiliation(s)
| | | | | | | | | | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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