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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Lin XB, Liu T, Schmaltz R, Ramer-Tait AE, Walter JW, Gänzle MG. Competitiveness of reutericyclin producing and nonproducing Limosilactobacillus reuteri in food and intestinal ecosystems: a game of rock, paper, and scissors? Lett Appl Microbiol 2024; 77:ovae007. [PMID: 38244231 DOI: 10.1093/lambio/ovae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
The ecological relationships among antimicrobial producing, resistant, and sensitive strains have been proposed to follow rock-paper-scissors dynamics, but evidence is mainly based on Gram-negative bacteriocins in vitro. The ecological relevance of antimicrobials in vivo or in situ has not been systematically studied. This study therefore aimed to analyze binary and ternary competitions among reutericyclin-producing strain Limosilactobacillus reuteri TMW1.656, its reutericyclin-resistant, nonproducing isogenic derivative L. reuteri TMW1.656∆rtcN, and the reutericyclin-sensitive, nonproducing L. reuteri TMW1.656∆rtcN∆rtcT in vitro (liquid culture and static plate), in situ (sourdough fermentation), and in vivo (gut of germ-free mice). In liquid culture, L. reuteri TMW1.656 had a higher fitness than TMW1.656∆rtcN and TMW1.656∆rtcN∆rtcT. Limosilactobacillus reuteri TMW1.656∆rtcN∆rtcT had a higher fitness than TMW1.656∆rtcN. On agar plates, L. reuteri TMW1.656 had a higher fitness than TMW1.656∆rtcN∆rtcT. In situ, reutericyclin production and resistance had no influence on the fitness of the strains. In vivo, TMW1.656 had an advantage over TMW1.656∆rtcN and TMW1.656∆rtcN∆rtcT. Ternary competitions showed reutericyclin production was ecologically beneficial in all ecosystems. The findings support the ecological importance of reutericyclin in a variety of environments/niches, providing an explanation for the acquisition of the reutericyclin gene cluster in L. reuteri and its contribution to the ecological fitness of Streptococcus mutans.
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Affiliation(s)
- Xiaoxi B Lin
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
| | - Tingting Liu
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
| | - Robert Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, United States
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68508, United States
| | - Jens W Walter
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
| | - Michael G Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
- Dept. of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, P.R. China
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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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Danhof HA, Lee J, Thapa A, Britton RA, Di Rienzi SC. Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling. Gut Microbes 2023; 15:2256043. [PMID: 37698879 PMCID: PMC10498800 DOI: 10.1080/19490976.2023.2256043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/11/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for L. reuteri-mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We find that L. reuteri facilitates oxytocin secretion from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells, while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri. This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.
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Affiliation(s)
- Heather A. Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Aanchal Thapa
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Sara C. Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
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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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Rajput A, Chauhan SM, Mohite OS, Hyun JC, Ardalani O, Jahn LJ, Sommer MO, Palsson BO. Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family. Food Microbiol 2023; 115:104334. [PMID: 37567624 DOI: 10.1016/j.fm.2023.104334] [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: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Omkar S Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Omid Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
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Zhang Y, Liao G, Wang M, Zhang Z, Liu L, Song Y, Wang D, Hao T, Feng J, Xia B, Wang Y, Tang X, Chen Y. Human-associated bacteria adopt an unusual route for synthesizing 3-acetylated tetramates for environmental adaptation. MICROBIOME 2023; 11:97. [PMID: 37147735 PMCID: PMC10161427 DOI: 10.1186/s40168-023-01548-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/11/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Tetramates or tetramic acid-containing compounds (TACs) are a group of bioactive natural products featuring a pyrrolidine-2,4-dione ring acknowledged being closed via Dieckmann cyclization. The cariogenic Streptococcus mutans strains bearing a muc biosynthetic gene cluster (BGC) can synthesize mutanocyclin (MUC), a 3-acetylated TAC that can inhibit both leukocyte chemotaxis and filamentous development in Candida albicans. Some strains can also accumulate reutericyclins (RTCs), the intermediates of MUC biosynthesis with antibacterial activities. However, the formation mechanism of the pyrrolidine-2,4-dione ring of MUC and the distribution of muc-like BGCs along with their ecological functions has not been explored extensively. RESULTS We demonstrated that a key intermediate of MUC biosynthesis, M-307, is installed by a hybrid nonribosomal peptide synthetase-polyketide synthase assembly line and its pyrrolidine-2,4-dione ring is closed via an unprecedented lactam bond formation style. Subsequent C-3 acetylation will convert M-307 to RTCs, which is then hydrolyzed by a deacylase, MucF, to remove the N-1 fatty acyl appendage to generate MUC. Distribution analysis showed that the muc-like BGCs distribute predominantly in human-associated bacteria. Interestingly, most of the muc-like BGCs possessing a mucF gene were isolated from human or livestock directly, indicating their involvement in alleviating the host's immune attacks by synthesizing MUC; while those BGCs lacking mucF gene distribute mainly in bacteria from fermented products, suggesting that they tend to synthesize RTCs to compete with neighboring bacteria. It is noteworthy that many bacteria in the same habitats (e.g., the oral cavity) lack the muc-like BGC, but possess functional MucF homologues to "detoxify" RTCs to MUC, including several competitive bacteria of S. mutans. We also comparably studied the distribution of TAS1, a fungal enzyme responsible for the production of phytotoxic tenuazonic acids (TeAs), a class of 3-acetylated TACs with similar structure but distinct biosynthetic mechanism to MUC, and found that it mainly exists in plants or crops. CONCLUSIONS The in vivo and in vitro experiments revealed that the pyrrolidine-2,4-dione ring of MUC is closed via lactam bond formation, which may be adopted by many TACs without 3-acyl decorations. Besides, we found that muc-like BGCs are widespread in human-associated bacteria and their shapes and main products can be influenced by the habitat environment and vice versa. By comparing with TeAs, we provided thought-provoking insights into how ecological and evolutionary forces drive bacteria and fungi to construct a common 3-acetylated pyrrolidine-2,4-dione core through different routes, and how the biosynthetic processes are delicately controlled to generate diverse 3-acetylated TACs for environmental adaptation. Video Abstract.
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Affiliation(s)
- Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ge Liao
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Min Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, Guangdong, China
| | - Zhao Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, 100034, China
| | - Liwei Liu
- Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dacheng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Hao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Xia
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Yixiang Wang
- Central Laboratory Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China.
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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