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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: 4] [Impact Index Per Article: 4.0] [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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Matsuzaki C, Takagi H, Saiga S, Kinoshita Y, Yamaguchi M, Higashimura Y, Yamamoto K, Yamaguchi M. Prebiotic effect of galacto- N-biose on the intestinal lactic acid bacteria as enhancer of acetate production and hypothetical colonization. Appl Environ Microbiol 2024; 90:e0144523. [PMID: 38411084 PMCID: PMC10952502 DOI: 10.1128/aem.01445-23] [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: 08/22/2023] [Accepted: 01/28/2024] [Indexed: 02/28/2024] Open
Abstract
Galacto-N-biose (GNB) is an important core structure of glycan of mucin glycoproteins in the gastrointestinal (GI) mucosa. Because certain beneficial bacteria inhabiting the GI tract, such as bifidobacteria and lactic acid bacteria, harbor highly specialized GNB metabolic capabilities, GNB is considered a promising prebiotic for nourishing and manipulating beneficial bacteria in the GI tract. However, the precise interactions between GNB and beneficial bacteria and their accompanying health-promoting effects remain elusive. First, we evaluated the proliferative tendency of beneficial bacteria and their production of beneficial metabolites using gut bacterial strains. By comparing the use of GNB, glucose, and inulin as carbon sources, we found that GNB enhanced acetate production in Lacticaseibacillus casei, Lacticaseibacillus rhamnosus, Lactobacillus gasseri, and Lactobacillus johnsonii. The ability of GNB to promote acetate production was also confirmed by RNA-seq analysis, which indicated the upregulation of gene clusters that catalyze the deacetylation of N-acetylgalactosamine-6P and biosynthesize acetyl-CoA from pyruvate, both of which result in acetate production. To explore the in vivo effect of GNB in promoting acetate production, antibiotic-treated BALB/cA mice were administered with GNB with L. rhamnosus, resulting in a fecal acetate content that was 2.7-fold higher than that in mice administered with only L. rhamnosus. Moreover, 2 days after the last administration, a 3.7-fold higher amount of L. rhamnosus was detected in feces administered with GNB with L. rhamnosus than in feces administered with only L. rhamnosus. These findings strongly suggest the prebiotic potential of GNB in enhancing L. rhamnosus colonization and converting L. rhamnosus into higher acetate producers in the GI tract. IMPORTANCE Specific members of lactic acid bacteria, which are commonly used as probiotics, possess therapeutic properties that are vital for human health enhancement by producing immunomodulatory metabolites such as exopolysaccharides, short-chain fatty acids, and bacteriocins. The long residence time of probiotic lactic acid bacteria in the GI tract prolongs their beneficial health effects. Moreover, the colonization property is also desirable for the application of probiotics in mucosal vaccination to provoke a local immune response. In this study, we found that GNB could enhance the beneficial properties of intestinal lactic acid bacteria that inhabit the human GI tract, stimulating acetate production and promoting intestinal colonization. Our findings provide a rationale for the addition of GNB to lactic acid bacteria-based functional foods. This has also led to the development of therapeutics supported by more rational prebiotic and probiotic selection, leading to an improved healthy lifestyle for humans.
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Affiliation(s)
- Chiaki Matsuzaki
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Hiroki Takagi
- Department of Production Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Sorachi Saiga
- Department of Production Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yuun Kinoshita
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Misako Yamaguchi
- Department of Organic Bio Chemistry, Faculty of Education, Wakayama University, Wakayama, Japan
| | - Yasuki Higashimura
- Department of Food Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Kenji Yamamoto
- Center for Innovative and Joint Research, Wakayama University, Wakayama, Japan
| | - Masanori Yamaguchi
- Department of Organic Bio Chemistry, Faculty of Education, Wakayama University, Wakayama, Japan
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Qiao N, Gaur G, Modesto M, Chinnici F, Scarafile D, Borruso L, Marin AC, Spiezio C, Valente D, Sandri C, Gänzle MG, Mattarelli P. Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar. J Appl Microbiol 2023; 134:lxad255. [PMID: 37934609 DOI: 10.1093/jambio/lxad255] [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: 04/25/2023] [Revised: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
AIMS Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris. METHODS AND RESULTS Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype. CONCLUSIONS Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.
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Affiliation(s)
- Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Gautam Gaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Fabio Chinnici
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano-Bozen, Bolzano 39100, Italy
| | - Antonio Castro Marin
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva, Bussolengo (Verona) 37012, Italy
| | - Daria Valente
- Department of Life Sciences and Systems Biology, University of Torino, Turin 10124, Italy
| | - Camillo Sandri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
- Department of Animal Health Care and Management, Parco Natura Viva, Bussolengo (Verona) 37012, Italy
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
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Ene A, Banerjee S, Wolfe AJ, Putonti C. Exploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris. mSphere 2023; 8:e0056222. [PMID: 37366621 PMCID: PMC10449518 DOI: 10.1128/msphere.00562-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences. Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).
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Affiliation(s)
- Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Swarnali Banerjee
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
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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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Yu L, Zang X, Chen Y, Gao Y, Pei Z, Yang B, Zhang H, Narbad A, Tian F, Zhai Q, Chen W. Phenotype-genotype analysis of Latilactobacills curvatus from different niches: Carbohydrate metabolism, antibiotic resistance, bacteriocin, phage fragments and linkages with CRISPR-Cas systems. Food Res Int 2022; 160:111640. [PMID: 36076376 DOI: 10.1016/j.foodres.2022.111640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
Abstract
The potential probiotic function of Latilactobacills curvatus has attracted the attention of researchers. To explore the differences in the genomes of L. curvatus, nine strains were isolated from various sources, including feces and fermented vegetables and compared with 25 strains from the NCBI database. The findings indicated that the average genome size, GC content, and CDS of L. curvatus were 1.94 MB, 41.9%, and 1825, respectively. Its core genome is associated with transcription, translation, carbohydrate transport and metabolism, and defense functions. The pan-genome of L. curvatus was in a closed state. The genetic diversity of L. curatus is mainly manifested in its ability to use carbohydrates, antibiotic resistance, bacteriocin operon, and polymeric regularly interspaced short palindromic repeats (CRISPR)-Cas for bacterial immunity. The CRISPR system of 34 strains of L. curvatus was predominantly found to be of the IIA type with a few IIC and IE types. These findings will contribute to a better understanding of this species.
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Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaojie Zang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ying Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuhang Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Arjan Narbad
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China; Gut Health and Microbiome Institute Strategic Programme, Quadram Institute Bioscience, Norwich 16 NR4 7UQ, UK
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
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Yu L, Chen Y, Duan H, Qiao N, Wang G, Zhao J, Zhai Q, Tian F, Chen W. Latilactobacillus sakei: a candidate probiotic with a key role in food fermentations and health promotion. Crit Rev Food Sci Nutr 2022; 64:978-995. [PMID: 35997270 DOI: 10.1080/10408398.2022.2111402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Latilactobacillus sakei is used extensively in industrial production and food fermentations. The species is primarily derived from fermented meat and vegetable products and is also found in human feces. Genomics and metabolomics have revealed unique metabolic pathways in L. sakei and molecular mechanisms underlying its competitive advantages in different habitats, which are mostly attributed to its flexible carbohydrate metabolism, cold tolerance, acid and salt tolerance, ability to cope with oxygen changes, and heme uptake. In recent years, probiotic effects of L. sakei and its metabolites have been identified, including the ability to effectively alleviate metabolic syndrome, inflammatory bowel disease, and atopic dermatitis. This review summarizes the genomic and metabolic characteristics of L. sakei and its metabolites and describes their applications, laying a foundation for their expanded use across the food and healthcare industries.
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Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Ying Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hui Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Gang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
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Abstract
Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary recommendations are fundamentally important for health promotion. Despite the importance of the human gut microbiota for the physiological effects of diet and chronic disease etiology, national dietary guidelines around the world are just beginning to capitalize on scientific breakthroughs in the microbiome field. In this review, we discuss contemporary nutritional recommendations from a microbiome science perspective, focusing on mechanistic evidence that established host-microbe interactions as mediators of the physiological effects of diet. We apply this knowledge to inform discussions of nutrition controversies, advance innovative dietary strategies, and propose an experimental framework that integrates the microbiome into nutrition research. The congruence of key paradigms in the nutrition and microbiome disciplines validates current recommendations in dietary guidelines, and the systematic incorporation of microbiome science into nutrition research has the potential to further improve and innovate healthy eating.
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Hitch TCA, Hall LJ, Walsh SK, Leventhal GE, Slack E, de Wouters T, Walter J, Clavel T. Microbiome-based interventions to modulate gut ecology and the immune system. Mucosal Immunol 2022; 15:1095-1113. [PMID: 36180583 PMCID: PMC9705255 DOI: 10.1038/s41385-022-00564-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 02/04/2023]
Abstract
The gut microbiome lies at the intersection between the environment and the host, with the ability to modify host responses to disease-relevant exposures and stimuli. This is evident in how enteric microbes interact with the immune system, e.g., supporting immune maturation in early life, affecting drug efficacy via modulation of immune responses, or influencing development of immune cell populations and their mediators. Many factors modulate gut ecosystem dynamics during daily life and we are just beginning to realise the therapeutic and prophylactic potential of microbiome-based interventions. These approaches vary in application, goal, and mechanisms of action. Some modify the entire community, such as nutritional approaches or faecal microbiota transplantation, while others, such as phage therapy, probiotics, and prebiotics, target specific taxa or strains. In this review, we assessed the experimental evidence for microbiome-based interventions, with a particular focus on their clinical relevance, ecological effects, and modulation of the immune system.
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Affiliation(s)
- Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich, UK
- Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Sarah Kate Walsh
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
- APC Microbiome Ireland, School of Microbiology and Department of Medicine, University College Cork, Cork, Ireland
| | | | - Emma Slack
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Jens Walter
- APC Microbiome Ireland, School of Microbiology and Department of Medicine, University College Cork, Cork, Ireland
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany.
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Lee JY, Bae E, Kim HY, Lee KM, Yoon SS, Lee DC. High-Fat-Diet-Induced Oxidative Stress Linked to the Increased Colonization of Lactobacillus sakei in an Obese Population. Microbiol Spectr 2021; 9:e0007421. [PMID: 34190593 PMCID: PMC8552675 DOI: 10.1128/spectrum.00074-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/24/2021] [Indexed: 11/20/2022] Open
Abstract
Obesity is a major public health problem related to various chronic health conditions. Lactobacillus species has been reported in obese individuals; however, its role is unknown. We compared the abundance and composition of Lactobacillus species by analyzing feces from 64 healthy control subjects and 88 obese subjects. We isolated one Lactobacillus strain from the feces of a subject with obesity and further analyzed its genetic and molecular features. We found that an increased abundance and higher prevalence of Lactobacillus sakei distinguished the fecal microbiota of the obese group from that of healthy subjects and that it was related to the increased levels of reactive oxygen species (ROS) induced by higher fat intake. The L. sakei ob4.1 strain, isolated from the feces of a subject with obesity, showed high catalase activity, which was regulated by oxidative stress at the gene transcription level. L. sakei ob4.1 maintained colon epithelial cell adhesion ability under ROS stimulation, and treatment with saturated fatty acid increased colon epithelial ROS levels in a dose-dependent manner; however, L. sakei ob4.1 did not change the level of fat-induced colon epithelial ROS. Exposing mice to a high-fat diet revealed that high-fat-diet-induced colon ROS was associated with the increased colonization of L. sakei ob4.1 through catalase activity. Four-week supplementation with this strain in mice fed a high-fat diet did not change their body weights or ROS levels. A high-fat diet induces changes in the colon environment by increasing ROS levels, which provides a colonization benefit to an L. sakei strain with high catalase activity. IMPORTANCELactobacillus provides many health benefits; its various species are widely used as probiotics. However, an increased abundance of Lactobacillus has been reported in obesity, and the role of Lactobacillus strains in obesity remains unknown. We found a high abundance of the Lactobacillus sakei species in a group of obese subjects and examined its relationship with a high-fat diet and reactive oxygen species (ROS) in the feces. To find the underlying mechanism, we analyzed and characterized an L. sakei strain isolated from a severely obese individual. We found that higher gut oxidative stress could link high-fat-diet-induced obesity and L. sakei. This translational research identifies the roles of the host gut environment in the colonization and survival of L. sakei.
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Affiliation(s)
- Jee-Yon Lee
- Department of Family Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Chaum Life Center, CHA Bundang Medical Center, School of Medicine, CHA University, Seoul, Republic of Korea
| | - Eunsoo Bae
- Chaum Life Center, CHA Bundang Medical Center, School of Medicine, CHA University, Seoul, Republic of Korea
| | - Hwa Young Kim
- Department of Microbiology and Immunology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Kang-Mu Lee
- Department of Microbiology and Immunology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea
| | - Duk-Chul Lee
- Department of Family Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
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11
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Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches. Foods 2021; 10:foods10081717. [PMID: 34441495 PMCID: PMC8393274 DOI: 10.3390/foods10081717] [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: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.
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12
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Managing the Microbiome: How the Gut Influences Development and Disease. Nutrients 2020; 13:nu13010074. [PMID: 33383647 PMCID: PMC7823600 DOI: 10.3390/nu13010074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
The microbiome lies at the forefront of scientific research, as researchers work to uncover its mysterious influence on human development and disease. This paper reviews how the microbiome is studied, how researchers can improve its study, and what clinical applications microbiome research might yield. For this review, we analyzed studies concerning the role of the microbiome in disease and early development, the common methodologies by which the microbiome is researched in the lab, and modern clinical treatments for dysbiosis and their possible future applications. We found that the gut microbiome is essential for proper development of various physiological systems and that gut dysbiosis is a clear factor in the etiology of various diseases. Furthermore, we found that germ-free animal models and microbiome manipulation techniques are inadequate, reducing the efficacy of microbiome research. Nonetheless, research continues to show the significance of microbiome manipulation in the clinical treatment of disease, having shown great promise in the prevention and treatment of dysbiosis. Though the clinical applications of microbiome manipulation are currently limited, the significance of dysbiosis in the etiology of a wide array of diseases indicates the significance of this research and highlights the need for more effective research methods concerning the microbiome.
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13
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Zhai Q, Shen X, Cen S, Zhang C, Tian F, Zhao J, Zhang H, Xue Y, Chen W. Screening of Lactobacillus salivarius strains from the feces of Chinese populations and the evaluation of their effects against intestinal inflammation in mice. Food Funct 2020; 11:221-235. [PMID: 31915776 DOI: 10.1039/c9fo02116g] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lactobacillus salivarius is a species of lactic acid bacteria with probiotic potency. Compared to such well-known probiotics as L. rhamnosus and L. casei, the genomic characteristics and health-beneficial effects of L. salivarius are inadequately researched. For this study, a medium with enhanced selectivity for the isolation of L. salivarius was developed by optimizing the carbon source and antibiotics in the medium. Seventy-three L. salivarius strains were isolated from 472 fecal samples from Chinese populations, and their pan-genomic and phylogenetic characterizations were analyzed. Three strains (L. salivarius HN26-4, NT4-8, and FXJCJ7-2) that were clearly categorized in different sub-phylotypes of the phylogenetic tree were randomly selected for further studies. Compared to the other two tested strains, L. salivarius FXJCJ7-2 showed higher tolerance to simulated gastrointestinal tract conditions and more significant anti-inflammatory effects in lipopolysaccharides (LPS)-treated RAW264.7 murine macrophages. This strain was also more effective in reversing LPS-induced alterations in gut barrier function, colonic histopathology, Treg/Th-17 balance, immunomodulatory indicators, nuclear factor kappa B pathway activation, and the intestinal microenvironment of the mice than the other two tested strains. Comparative genomic analysis indicated that these protective effects may be related to the specific genes of L. salivarius FXJCJ7-2 that were involved in the tolerance to the gastrointestinal environment, short-chain fatty acid production, and host-bacterium interaction.
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Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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14
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Chen Y, Yu L, Qiao N, Xiao Y, Tian F, Zhao J, Zhang H, Chen W, Zhai Q. Latilactobacillus curvatus: A Candidate Probiotic with Excellent Fermentation Properties and Health Benefits. Foods 2020; 9:E1366. [PMID: 32993033 PMCID: PMC7600897 DOI: 10.3390/foods9101366] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 02/02/2023] Open
Abstract
Latilactobacillus curvatus is a candidate probiotic that has been included in the list of recommended biological agents for certification by the European Food Safety Authority. According to the published genomic information, L. curvatus has several genes that encode metabolic pathways of carbohydrate utilization. In addition, there are some differences in cell surface complex related genes of L. curvatus from different sources. L. curvatus also has several genes that encode bacteriocin production, which can produce Curvacin A and Sakacin P. Due to its ability to produce bacteriocin, it is often used as a bioprotective agent in fermented meat products, to inhibit the growth of a variety of pathogenic and spoilage bacteria. L. curvatus exerts some probiotic effects, such as mediating the production of IL-10 by dendritic cells through NF-κB and extracellular regulated protein kinases (ERK) signals to relieve colitis in mice. This review is the first summary of the genomic and biological characteristics of L. curvatus. Our knowledge on its role in the food industry and human health is also discussed, with the aim of providing a theoretical basis for the development of applications of L. curvatus.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi 214122, China
| | - Nanzhen Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (L.Y.); (Y.C.); (N.Q.); (Y.X.); (F.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi 214122, China
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15
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De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
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16
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Gastrointestinal survival and potential bioactivities of Lactobacillus curieae CCTCC M2011381 in the fermentation of plant food. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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An Acid Up-Regulated Surface Protein of Lactobacillus paracasei Strain GCRL 46 is Phylogenetically Related to the Secreted Glucan- (GpbB) and Immunoglobulin-Binding (SibA) Protein of Pathogenic Streptococci. Int J Mol Sci 2019; 20:ijms20071610. [PMID: 30935131 PMCID: PMC6479570 DOI: 10.3390/ijms20071610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 02/07/2023] Open
Abstract
Bacterial cell wall hydrolases, including amidases and peptidases, play a critical role in peptidoglycan turnover during growth, impacting daughter cell separation, and cell death, through autolysis. When exploring the regulation of protein expression across the growth cycle of an acid-resistant strain of Lactobacillus paracasei, GCRL 46, we observed temporal up-regulation of proteins in the 40⁻45 kDa molecular weight range for whole-cell extracts when culturing in fermenters at a controlled pH of 4.0 versus optimum growth pH of 6.3. Up-regulation of proteins in this size range was not detected in SDS-PAGE gels of the cytosolic fraction, but was routinely detected following growth at low pH in whole cells and cell debris obtained after bead beating and centrifugation, indicating a cell surface location. N-terminal sequencing and in silico analyses showed sequence similarity with proteins in the L. casei group (L. casei, L. paracasei and L. rhamnosus) which were variously annotated as uncharacterized proteins, surface antigens, possible TrsG proteins, CHAP (cysteine, histidine-dependent amidohydrolases/peptidases)-domain proteins or putative peptidoglycan d,l-endopeptidase due to the presence of a CwlO domain. This protein is a homologue of the p40 (Msp2) secreted protein of L. rhamnosus LGG, which is linked to probiotic functionality in this species, and is phylogenetically related to structurally-similar proteins found in Enterococcus, Streptococcus and Bifidobacterium species, including the glucan-binding (GbpB), surface antigen (SagA) proteins detected in pathogenic group A streptococci species as secreted, immunoglobulin-binding (SibA) proteins (also named PcsB). Three-dimensional (3D) modelling predicted structural similarities in the CHAP proteins from the L. casei group and streptococcal species, indicating retention of overall architecture despite sequence divergence, and an implied retention of function during evolution. A phylogenetically-related hydrolase also contained the CwlO domain with a NLPC_P60 domain, and showed similar overall but distinct architecture to the CHAP proteins. We concluded that the surface-located, CHAP protein in L. casei is up-regulated during long-term exposure to acidic conditions during growth but not during acid shock.
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18
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Kok CR, Hutkins R. Yogurt and other fermented foods as sources of health-promoting bacteria. Nutr Rev 2018; 76:4-15. [DOI: 10.1093/nutrit/nuy056] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Car Reen Kok
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
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19
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Terán LC, Coeuret G, Raya R, Zagorec M, Champomier-Vergès MC, Chaillou S. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome Biol Evol 2018; 10:1516-1525. [PMID: 29850855 PMCID: PMC6007345 DOI: 10.1093/gbe/evy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
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Affiliation(s)
- Lucrecia C Terán
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Gwendoline Coeuret
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Raúl Raya
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | | | - Stéphane Chaillou
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
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20
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Rezac S, Kok CR, Heermann M, Hutkins R. Fermented Foods as a Dietary Source of Live Organisms. Front Microbiol 2018; 9:1785. [PMID: 30197628 PMCID: PMC6117398 DOI: 10.3389/fmicb.2018.01785] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/17/2018] [Indexed: 01/08/2023] Open
Abstract
The popularity of fermented foods and beverages is due to their enhanced shelf-life, safety, functionality, sensory, and nutritional properties. The latter includes the presence of bioactive molecules, vitamins, and other constituents with increased availability due to the process of fermentation. Many fermented foods also contain live microorganisms that may improve gastrointestinal health and provide other health benefits, including lowering the risk of type two diabetes and cardiovascular diseases. The number of organisms in fermented foods can vary significantly, depending on how products were manufactured and processed, as well as conditions and duration of storage. In this review, we surveyed published studies in which lactic acid and other relevant bacteria were enumerated from the most commonly consumed fermented foods, including cultured dairy products, cheese, fermented sausage, fermented vegetables, soy-fermented foods, and fermented cereal products. Most of the reported data were based on retail food samples, rather than experimentally produced products made on a laboratory scale. Results indicated that many of these fermented foods contained 105-7 lactic acid bacteria per mL or gram, although there was considerable variation based on geographical region and sampling time. In general, cultured dairy products consistently contained higher levels, up to 109/mL or g. Although few specific recommendations and claim legislations for what constitutes a relevant dose exist, the findings from this survey revealed that many fermented foods are a good source of live lactic acid bacteria, including species that reportedly provide human health benefits.
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Affiliation(s)
| | | | | | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln, NE, United States
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21
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Affiliation(s)
- M. E. Sanders
- International Scientific Association for Probiotics and Prebiotics; Centennial CO USA
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22
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Leroy F, Aymerich T, Champomier-Vergès MC, Cocolin L, De Vuyst L, Flores M, Leroi F, Leroy S, Talon R, Vogel RF, Zagorec M. Fermented meats (and the symptomatic case of the Flemish food pyramid): Are we heading towards the vilification of a valuable food group? Int J Food Microbiol 2018; 274:67-70. [DOI: 10.1016/j.ijfoodmicro.2018.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 02/01/2023]
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23
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Zagorec M, Champomier-Vergès MC. Lactobacillus sakei: A Starter for Sausage Fermentation, a Protective Culture for Meat Products. Microorganisms 2017; 5:microorganisms5030056. [PMID: 28878171 PMCID: PMC5620647 DOI: 10.3390/microorganisms5030056] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 12/28/2022] Open
Abstract
Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture. The emerging exploration of the microbial ecology of meat products also revealed the multiplicity of bacterial interactions L. sakei has to face and their various consequences on microbial quality and safety at the end of storage.
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Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Pérez-Muñoz ME, Leulier F, Gänzle M, Walter J. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev 2017; 41:S27-S48. [DOI: 10.1093/femsre/fux030] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/06/2017] [Indexed: 02/07/2023] Open
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25
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Rossi M, Martínez-Martínez D, Amaretti A, Ulrici A, Raimondi S, Moya A. Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:399-406. [PMID: 27043715 DOI: 10.1111/1758-2229.12405] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/08/2016] [Indexed: 02/05/2023]
Abstract
The genus Lactobacillus includes over 215 species that colonize plants, foods, sewage and the gastrointestinal tract (GIT) of humans and animals. In the GIT, Lactobacillus population can be made by true inhabitants or by bacteria occasionally ingested with fermented or spoiled foods, or with probiotics. This study longitudinally surveyed Lactobacillus species and strains in the feces of a healthy subject through whole genome sequencing (WGS) data-mining, in order to identify members of the permanent or transient populations. In three time-points (0, 670 and 700 d), 58 different species were identified, 16 of them being retrieved for the first time in human feces. L. rhamnosus, L. ruminis, L. delbrueckii, L. plantarum, L. casei and L. acidophilus were the most represented, with estimated amounts ranging between 6 and 8 Log (cells g(-1) ), while the other were detected at 4 or 5 Log (cells g(-1) ). 86 Lactobacillus strains belonging to 52 species were identified. 43 seemingly occupied the GIT as true residents, since were detected in a time span of almost 2 years in all the three samples or in 2 samples separated by 670 or 700 d. As a whole, a stable community of lactobacilli was disclosed, with wide and understudied biodiversity.
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Affiliation(s)
- Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniel Martínez-Martínez
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandro Ulrici
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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26
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Shin SY, Han NS. Leuconostoc spp. as Starters and Their Beneficial Roles in Fermented Foods. BENEFICIAL MICROORGANISMS IN FOOD AND NUTRACEUTICALS 2015. [DOI: 10.1007/978-3-319-23177-8_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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27
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Abstract
Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.
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Benmechernene Z, Fernández-No I, Quintela-Baluja M, Böhme K, Kihal M, Calo-Mata P, Barros-Velázquez J. Genomic and proteomic characterization of bacteriocin-producing Leuconostoc mesenteroides strains isolated from raw camel milk in two southwest Algerian arid zones. BIOMED RESEARCH INTERNATIONAL 2014; 2014:853238. [PMID: 24809059 PMCID: PMC3997938 DOI: 10.1155/2014/853238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 11/24/2022]
Abstract
Information on the microbiology of camel milk is very limited. In this work, the genetic characterization and proteomic identification of 13 putative producing bacteriocin Leuconostoc strains exhibiting antilisterial activity and isolated from camel milk were performed. DNA sequencing of the 13 selected strains revealed high homology among the 16S rRNA genes for all strains. In addition, 99% homology with Leuconostoc mesenteroides was observed when these sequences were analysed by the BLAST tool against other sequences from reference strains deposited in the Genbank. Furthermore, the isolates were characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDITOF MS) which allowed for the identification of 2 mass peaks 6242 m/z and 5118 m/z that resulted to be specific to the species L. mesenteroides. Remarkably, the phyloproteomic tree provided more intraspecific information of L. mesenteroides than phylogenetic analysis. Accordingly, phyloproteomic analysis grouped L. mesenteroides strains into different subbranches, while all L. mesenteroides isolates were grouped in the same branch according to phylogenetic analysis. This study represents, to our knowledge, the first report on the use of MALDI-TOF MS on the identification of LAB isolated from camel milk.
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Affiliation(s)
- Zineb Benmechernene
- Laboratory of Applied Microbiology, Department of Biology, Faculty of Sciences, Oran University, B.P. 16, 31100 Es-Senia, Oran, Algeria
| | - Inmaculada Fernández-No
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, 27002 Lugo, Spain
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, 27002 Lugo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, 27002 Lugo, Spain
| | - Mebrouk Kihal
- Laboratory of Applied Microbiology, Department of Biology, Faculty of Sciences, Oran University, B.P. 16, 31100 Es-Senia, Oran, Algeria
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, 27002 Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, 27002 Lugo, Spain
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Population genetics of Lactobacillus sakei reveals three lineages with distinct evolutionary histories. PLoS One 2013; 8:e73253. [PMID: 24069179 PMCID: PMC3777942 DOI: 10.1371/journal.pone.0073253] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/19/2013] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products.
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Anba-Mondoloni J, Chaillou S, Zagorec M, Champomier-Vergès MC. Catabolism of N-acetylneuraminic acid, a fitness function of the food-borne lactic acid bacterium Lactobacillus sakei, involves two newly characterized proteins. Appl Environ Microbiol 2013; 79:2012-8. [PMID: 23335758 PMCID: PMC3592224 DOI: 10.1128/aem.03301-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/11/2013] [Indexed: 01/27/2023] Open
Abstract
In silico analysis of the genome sequence of the meat-borne lactic acid bacterium (LAB) Lactobacillus sakei 23K has revealed a repertoire of potential functions related to the adaptation of this bacterium to the meat environment. Among these functions, the ability to use N-acetyl-neuraminic acid (NANA) as a carbon source could provide a competitive advantage for growth on meat in which this amino sugar is present. In this work, we proposed to analyze the functionality of a gene cluster encompassing nanTEAR and nanK (nanTEAR-nanK). We established that this cluster encoded a pathway allowing transport and early steps of the catabolism of NANA in this genome. We also demonstrated that this cluster was absent from the genome of other L. sakei strains that were shown to be unable to grow on NANA. Moreover, L. sakei 23K nanA, nanT, nanK, and nanE genes were able to complement Escherichia coli mutants. Construction of different mutants in L. sakei 23K ΔnanR, ΔnanT, and ΔnanK and the double mutant L. sakei 23K Δ(nanA-nanE) made it possible to show that all were impaired for growth on NANA. In addition, two genes located downstream from nanK, lsa1644 and lsa1645, are involved in the catabolism of sialic acid in L. sakei 23K, as a L. sakei 23K Δlsa1645 mutant was no longer able to grow on NANA. All these results demonstrate that the gene cluster nanTEAR-nanK-lsa1644-lsa1645 is indeed involved in the use of NANA as an energy source by L. sakei.
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Bibiloni R. Rodent models to study the relationships between mammals and their bacterial inhabitants. Gut Microbes 2012; 3:536-43. [PMID: 22918304 PMCID: PMC3495791 DOI: 10.4161/gmic.21905] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Laboratory rodents have been instrumental in helping researchers to unravel the complex interactions that mammals have with their microbial commensals. Progress in defining these interactions has also been possible thanks to the development of culture-independent methods for describing the microbiota associated to body surfaces. Understanding the mechanisms that govern this relationship at the molecular, cellular, and ecological levels is central to both health and disease. The present review of rodent models commonly used to investigate microbial-host "conversations" is focused on those complex bacterial communities residing in the lower gut. Although many types of pathology have been studied using gnotobiotic animals, only the models relevant to commensal bacteria will be described.
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32
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Collins J, van Pijkeren JP, Svensson L, Claesson MJ, Sturme M, Li Y, Cooney JC, van Sinderen D, Walker AW, Parkhill J, Shannon O, O'Toole PW. Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein. Mol Microbiol 2012; 85:862-77. [PMID: 22724453 DOI: 10.1111/j.1365-2958.2012.08148.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The marketplace for probiotic foods is burgeoning, measured in billions of euro per annum. It is imperative, however, that all bacterial strains are fully assessed for human safety. The ability to bind fibrinogen is considered a potential pathogenicity trait that can lead to platelet aggregation, serious medical complications, and in some instances, death. Here we examined strains from species frequently used as probiotics for their ability to bind human fibrinogen. Only one strain (CCUG 47825), a Lactobacillus salivarius isolate from a case of septicaemia, was found to strongly adhere to fibrinogen. Furthermore, this strain was found to aggregate human platelets at a level comparable to the human pathogen Staphylococcus aureus. By sequencing the genome of CCUG 47825, we were able to identify candidate genes responsible for fibrinogen binding. Complementing the genetic analysis with traditional molecular microbiological techniques enabled the identification of the novel fibrinogen receptor, CCUG_2371. Although only strain CCUG 47825 bound fibrinogen under laboratory conditions, homologues of the novel fibrinogen binding gene CCUG_2371 are widespread among L. salivarius strains, maintaining their potential to bind fibrinogen if expressed. We highlight the fact that without a full genetic analysis of strains for human consumption, potential pathogenicity traits may go undetected.
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Affiliation(s)
- James Collins
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Guilbaud M, Zagorec M, Chaillou S, Champomier-Vergès MC. Intraspecies diversity of Lactobacillus sakei response to oxidative stress and variability of strain performance in mixed strains challenges. Food Microbiol 2012; 29:197-204. [DOI: 10.1016/j.fm.2011.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/13/2011] [Accepted: 07/20/2011] [Indexed: 11/26/2022]
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Lönnermark E, Nowrouzinan F, Adlerberth I, Ahrné S, Wold A, Friman V. Oral and faecal lactobacilli and their expression of mannose-specific adhesins in individuals with and without IgA deficiency. Int J Med Microbiol 2011; 302:53-60. [PMID: 22018813 DOI: 10.1016/j.ijmm.2011.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 07/21/2011] [Accepted: 08/29/2011] [Indexed: 01/23/2023] Open
Abstract
Lactobacilli are present in the intestine and oral cavity of most adults. Secretory IgA in mucosal secretions may provide carbohydrate receptors for bacterial adhesins. Here, oral and faecal samples from 33 IgA-deficient individuals and 34 controls were cultured for lactobacilli, which were identified using species-specific PCR or partial 16S rDNA sequencing and tested for expression of mannose-specific adhesins. Lactobacilli were found in the oral cavity of 76% of IgA-deficient and 85% of control individuals. Lactobacillus paracasei and Lactobacillus gasseri dominated in both groups. Lactobacillus fermentum was less common in IgA-deficient individuals than in controls (p=0.0055) and Lactobacillus salivarius was less common in symptomatic than in healthy IgA-deficient individuals (p=0.0051). Faecal samples yielded lactobacilli in most individuals. L. paracasei was most frequent, followed by L. gasseri and Lactobacillus plantarum. Mannose-specific adhesins were expressed more frequently by oral than by faecal isolates (p=0.032) and oral isolates adhered in higher numbers than faecal isolates (46 vs. 14 bacteria/cell, p=0.0038). Faecal isolates from IgA-deficient individuals more frequently expressed mannose-specific adhesins than faecal isolates from controls (p=0.039). Mannose-specific adhesins may be a colonisation factor in the oral cavity, and the presence of secretory IgA may modify adhesin expression. However, secretory IgA seems to have little influence on Lactobacillus species distribution.
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Affiliation(s)
- Elisabet Lönnermark
- Department of Infectious Diseases, Gothenburg University, S-41685 Göteborg, Sweden.
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35
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Lucquin I, Zagorec M, Champomier-Vergès M, Chaillou S. Fingerprint of lactic acid bacteria population in beef carpaccio is influenced by storage process and seasonal changes. Food Microbiol 2011; 29:187-96. [PMID: 22202872 DOI: 10.1016/j.fm.2011.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 08/01/2011] [Accepted: 08/03/2011] [Indexed: 10/17/2022]
Abstract
We have investigated the population structure of lactic acid bacteria (LAB) for several beef carpaccio available on the market with the purpose of comparing the effect of storage process (modified-atmosphere packaging and vacuum-packaging) and of seasonal changes on this microbial population. Out of 60 samples we have characterised 214 isolates accounting for 10 LAB species and 35 isolates accounting for 11 non-LAB species. Lactobacillus sakei, Leuconostoc carnosum and Leuconostoc mesenteroides were the most prevailing LAB species with a frequency of identification within 66%, 62% and 52% of the samples respectively. These 3 species were also characterised by a phenotypic intra-species diversity of isolates based on colony morphology. We showed that the prevalence was increased 1.5 fold for L. sakei and L. mesenteroides during the summer sampling in comparison to the spring or the fall sampling suggesting an environmental origin of these two species. Seasonal variations were also observed for the prevalence of Lactobacillus fuchuensis and L. carnosum in spring (2- and 1.5-fold increase, respectively) and of Brochothrix thermosphacta in fall (6-fold increase). Finally, we demonstrated that the growth potential after the sell-by-date was favourable of 1.25 log(10) cfu g(-1) to Leuconostoc spp. in modified-atmosphere packaging and of 1.38 log(10) cfu g(-1) to Lactobacillus spp. in vacuum-packaging. In conclusion, we show that important and unsuspected traits in bacterial population dynamics can be unravelled by large sampling strategies. We discuss about the need to take this assessment into account for further studies on bacterial ecosystems of meat.
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Affiliation(s)
- Isabelle Lucquin
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350 Jouy-en-Josas, France
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Mikelsaar M. Human microbial ecology: lactobacilli, probiotics, selective decontamination. Anaerobe 2011; 17:463-7. [PMID: 21787875 DOI: 10.1016/j.anaerobe.2011.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/07/2011] [Indexed: 12/20/2022]
Abstract
Health care-associated infections are closely associated with different medical interventions which interrupt the balance of human microbiota. The occasional predominance of opportunistic pathogens may lead to their translocation into the lymph nodes and bloodstream, causing endogenous (primary or secondary) hospital infections. The question is raised as to if there is a possibility for prevention of the imbalance of GI microbiota during medical interventions in critically ill patients. Prophylactic selective decontamination of the digestive tract (SDD) simultaneously applies three to four different antimicrobials for the suppression of enteric aerobic microbes, which are potentially pathogenic microorganisms. However, there is no convincing evidence that the indigenous beneficial intestinal microbiota are preserved, resulting in reduced mortality of high-risk patients. In this overview, we have evaluated the antimicrobial treatment guidelines of the Infectious Diseases Society of America (IDSA) for intra-abdominal infections in adults and seniors according to their safety for different Lactobacillus spp. The data from our group and in the literature have shown that all tested lactobacilli strains (nearly one hundred) were insusceptible to metronidazole while different species of lactobacilli of the three fermentation groups expressed particular antibiotic susceptibility to vancomycin, cefoxitin, ciprofloxacin and some new tetracyclines. We have relied on microbial ecology data showing that the GI tracts of adults and the elderly are simultaneously colonised at least with several (four to a maximum of 12) Lactobacillus species expressing variable intrinsic insusceptibility to the aforementioned antimicrobials, according to the provided data in table. This finding offers the possibility of preserving the colonisation of the intestine with some beneficial lactobacilli during antimicrobial treatment in critically ill patients with health care-associated infections. Several probiotic Lactobacillus spp. strains are intrinsically resistant to antimicrobials and can be used during antibacterial therapy, however, their application as an additive to antimicrobial treatment in critically ill patients needs to be investigated in well-designed clinical trials.
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Affiliation(s)
- Marika Mikelsaar
- Department of Microbiology, Medical Faculty, University of Tartu, Tartu 50411, Estonia.
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McLeod A, Snipen L, Naterstad K, Axelsson L. Global transcriptome response in Lactobacillus sakei during growth on ribose. BMC Microbiol 2011; 11:145. [PMID: 21702908 PMCID: PMC3146418 DOI: 10.1186/1471-2180-11-145] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lactobacillus sakei is valuable in the fermentation of meat products and exhibits properties that allow for better preservation of meat and fish. On these substrates, glucose and ribose are the main carbon sources available for growth. We used a whole-genome microarray based on the genome sequence of L. sakei strain 23K to investigate the global transcriptome response of three L. sakei strains when grown on ribose compared with glucose. RESULTS The function of the common regulated genes was mostly related to carbohydrate metabolism and transport. Decreased transcription of genes encoding enzymes involved in glucose metabolism and the L-lactate dehydrogenase was observed, but most of the genes showing differential expression were up-regulated. Especially transcription of genes directly involved in ribose catabolism, the phosphoketolase pathway, and in alternative fates of pyruvate increased. Interestingly, the methylglyoxal synthase gene, which encodes an enzyme unique for L. sakei among lactobacilli, was up-regulated. Ribose catabolism seems closely linked with catabolism of nucleosides. The deoxyribonucleoside synthesis operon transcriptional regulator gene was strongly up-regulated, as well as two gene clusters involved in nucleoside catabolism. One of the clusters included a ribokinase gene. Moreover, hprK encoding the HPr kinase/phosphatase, which plays a major role in the regulation of carbon metabolism and sugar transport, was up-regulated, as were genes encoding the general PTS enzyme I and the mannose-specific enzyme II complex (EIIman). Putative catabolite-responsive element (cre) sites were found in proximity to the promoter of several genes and operons affected by the change of carbon source. This could indicate regulation by a catabolite control protein A (CcpA)-mediated carbon catabolite repression (CCR) mechanism, possibly with the EIIman being indirectly involved. CONCLUSIONS Our data shows that the ribose uptake and catabolic machinery in L. sakei is highly regulated at the transcription level. A global regulation mechanism seems to permit a fine tuning of the expression of enzymes that control efficient exploitation of available carbon sources.
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Affiliation(s)
- Anette McLeod
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, NO-1430, Norway
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, Ås, NO-1432, Norway
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, Ås, NO-1432, Norway
| | - Kristine Naterstad
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, NO-1430, Norway
| | - Lars Axelsson
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, NO-1430, Norway
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Oki K, Kudo Y, Watanabe K. Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2011; 62:601-607. [PMID: 21515698 DOI: 10.1099/ijs.0.031658-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive strains, YIT 12363(T) and YIT 12364(T), were isolated from human faeces. They were rod-shaped, non-motile, asporogenous, facultatively anaerobic and did not exhibit catalase activity. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus casei (95.3% similarity), Lactobacillus paracasei subsp. paracasei (95.6%), Lactobacillus paracasei subsp. tolerans (95.3%) and Lactobacillus rhamnosus (95.4%) were the closest neighbours to strain YIT 12363(T). For strain YIT 12364(T), the highest similarity values were observed with the type strains of Lactobacillus diolivorans, Lactobacillus parafarraginis and Lactobacillus rapi (95.8, 96.0 and 96.0%, respectively). Phenotypic and genotypic features demonstrated that these strains each represent a separate novel species of the genus Lactobacillus, and the names Lactobacillus saniviri sp. nov. (type strain YIT 12363(T)=JCM 17471(T)=DSM 24301(T)) and Lactobacillus senioris sp. nov. (type strain YIT 12364(T)=JCM 17472(T)=DSM 24302(T)), respectively, are proposed.
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Affiliation(s)
- Kaihei Oki
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
| | - Yuko Kudo
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
| | - Koichi Watanabe
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
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Nyquist OL, McLeod A, Brede DA, Snipen L, Aakra Å, Nes IF. Comparative genomics of Lactobacillus sakei with emphasis on strains from meat. Mol Genet Genomics 2011; 285:297-311. [DOI: 10.1007/s00438-011-0608-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 02/08/2011] [Indexed: 02/06/2023]
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40
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Diversity and metabolic impact of intestinal Lactobacillus species in healthy adults and the elderly. Br J Nutr 2011; 105:1235-44. [PMID: 21303568 DOI: 10.1017/s0007114510004770] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The present study aimed at assessing the counts and species distribution of intestinal lactobacilli and exploring if the data are associated with BMI and blood glucose level in healthy adults and elderly persons. The BMI (P < 0·01), the level of fasting blood glucose (P < 0·001) and the total counts of lactobacilli (P < 0·01 by bacteriology; P < 0·001 by real-time PCR) were higher in the elderly. The number of species in adults was lower (P < 0·05), who were more often colonised with Lactobacillus acidophilus (P = 0·031) and L. helveticus (P < 0·001). In contrast, L. plantarum (P = 0·035), L. paracasei (P < 0·001) and L. reuteri (P = 0·031) were more prevalent in the elderly. L. rhamnosus was detected in adults (P < 0·001), but not in any elderly person. BMI was associated with counts of lactobacilli, adjusted for age and sex (P = 0·008). The higher BMI in both groups of persons was associated with the presence of obligate homofermentative lactobacilli and L. sakei, both adjusted for age and sex. Plasma glucose values were positively correlated with BMI and negatively correlated with colonisation with L. paracasei (P = 0·0238) in adults and on the borderline with L. fermentum (P = 0·052) in the elderly. Thus, the species-specific PCR analysis of Lactobacillus sp. combined with viable plating data indicates substantial age-related structural differences in the intestinal lactobacilli communities. The higher counts of intestinal Lactobacillus sp. are associated with higher BMI and blood glucose content, while their specific fermentative groups and species of lactobacilli appear at different glucose levels both in adults and in the elderly.
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Endo A, Futagawa-Endo Y, Dicks LMT. Diversity of Lactobacillus and Bifidobacterium in feces of herbivores, omnivores and carnivores. Anaerobe 2010; 16:590-6. [PMID: 21034840 DOI: 10.1016/j.anaerobe.2010.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/08/2010] [Accepted: 10/20/2010] [Indexed: 12/21/2022]
Abstract
The Lactobacillus and Bifidobacterium population in the feces of 26 animals (16 species) were studied by culture-dependent and culture-independent techniques. Lactobacilli were detected from a few herbivores, all carnivores and some omnivores. Lactobacillus johnsonii, Lactobacillus reuteri, Lactobacillus salivarius, Lactobacillus vaginalis and Lactobacillus ingluviei were the most dominant lactobacilli in carnivores. These species were, however, not predominant in herbivores and omnivores. Lactobacillus brevis, Lactobacillus casei, Lactobacillus parabuchneri, Lactobacillus plantarum, Lactobacillus sakei, Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides, usually present in raw plant material, were present in omnivores but not in carnivores. Bifidobacteria were detected in only four herbivores and two omnivores. Bifidobacterium pseudolongum was the only Bifidobacterium species detected in herbivores. Bifidobacteria detected in the two omnivores are phylogenetically not closely related to known species and are possible novel species in the genus.
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Affiliation(s)
- Akihito Endo
- Department of Microbiology, University of Stellenbosch, South Africa.
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Determining the genetic diversity of lactobacilli from the oral cavity. J Microbiol Methods 2010; 82:163-9. [PMID: 20573585 DOI: 10.1016/j.mimet.2010.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/14/2010] [Accepted: 05/21/2010] [Indexed: 11/20/2022]
Abstract
Several methods for determining the diversity of Lactobacillus spp were evaluated with the purpose of developing a realistic approach for further studies. The patient population was comprised of young children with an oral disease called severe early childhood caries. The ultimate goal of these studies was to ascertain the role of lactobacilli in the caries process. To accomplish that goal, we evaluated several methods and approaches for determining diversity including AP-PCR, chromosomal DNA fingerprinting, denaturing gradient gel electrophoresis, and 16S rRNA gene sequencing. Central to these methods was the gathering and screening of isolates from cultivation medium. Using various estimates of diversity, we addressed the question as to how many isolates represent the overall diversity and how cultivation compares to non-cultivation techniques. Finally, we proposed a working approach for achieving the goals outlined framed by both practical constraints in terms of time, effort and efficacy while yielding a reliable outcome.
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Chiaramonte F, Anglade P, Baraige F, Gratadoux JJ, Langella P, Champomier-Vergès MC, Zagorec M. Analysis of Lactobacillus sakei mutants selected after adaptation to the gastrointestinal tracts of axenic mice. Appl Environ Microbiol 2010; 76:2932-9. [PMID: 20208026 PMCID: PMC2863443 DOI: 10.1128/aem.02451-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 02/23/2010] [Indexed: 12/25/2022] Open
Abstract
We recently showed that Lactobacillus sakei, a natural meat-borne lactic acid bacterium, can colonize the gastrointestinal tracts (GIT) of axenic mice but that this colonization in the intestinal environment selects L. sakei mutants showing modified colony morphology (small and rough) and cell shape, most probably resulting from the accumulation of various mutations that confer a selective advantage for persistence in the GIT. In the present study, we analyzed such clones, issued from three different L. sakei strains, in order to determine which functions were modified in the mutants. In the elongated filamentous cells of the rough clones, transmission electron microscopy (TEM) analysis showed a septation defect and dotted and slanted black bands, suggesting the presence of a helical structure around the cells. Comparison of the cytoplasmic and cell wall/membrane proteomes of the meat isolate L. sakei 23K and of one of its rough derivatives revealed a modified expression for 38 spots. The expression of six oxidoreductases, several stress proteins, and four ABC transporters was strongly reduced in the GIT-adapted strain, while the actin-like MreB protein responsible for cell shaping was upregulated. In addition, the expression of several enzymes involved in carbohydrate metabolism was modified, which may correlate with the observation of modified growth of mutants on various carbon sources. These results suggest that the modifications leading to a better adaptation to the GIT are pleiotropic and are characterized in a rough mutant by a different stress status, a cell wall modification, and modified use of energy sources, leading to an improved fitness for the colonization of the GIT.
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Affiliation(s)
- Fabrizio Chiaramonte
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
| | - Patricia Anglade
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
| | - Fabienne Baraige
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
| | - Jean-Jacques Gratadoux
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
| | - Philippe Langella
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
| | - Marie-Christine Champomier-Vergès
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
| | - Monique Zagorec
- Unité Flore Lactique et Environnement Carné, UR309, Unité Ecologie et Physiologie du Système Digestif, UR902, INRA, Domaine de Vilvert, F78350 Jouy en Josas, France
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McLeod A, Zagorec M, Champomier-Vergès MC, Naterstad K, Axelsson L. Primary metabolism in Lactobacillus sakei food isolates by proteomic analysis. BMC Microbiol 2010; 10:120. [PMID: 20412581 PMCID: PMC2873491 DOI: 10.1186/1471-2180-10-120] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 04/22/2010] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Lactobacillus sakei is an important food-associated lactic acid bacterium commonly used as starter culture for industrial meat fermentation, and with great potential as a biopreservative in meat and fish products. Understanding the metabolic mechanisms underlying the growth performance of a strain to be used for food fermentations is important for obtaining high-quality and safe products. Proteomic analysis was used to study the primary metabolism in ten food isolates after growth on glucose and ribose, the main sugars available for L. sakei in meat and fish. RESULTS Proteins, the expression of which varied depending on the carbon source were identified, such as a ribokinase and a D-ribose pyranase directly involved in ribose catabolism, and enzymes involved in the phosphoketolase and glycolytic pathways. Expression of enzymes involved in pyruvate and glycerol/glycerolipid metabolism were also affected by the change of carbon source. Interestingly, a commercial starter culture and a protective culture strain down-regulated the glycolytic pathway more efficiently than the rest of the strains when grown on ribose. The overall two-dimensional gel electrophoresis (2-DE) protein expression pattern was similar for the different strains, though distinct differences were seen between the two subspecies (sakei and carnosus), and a variation of about 20% in the number of spots in the 2-DE gels was observed between strains. A strain isolated from fermented fish showed a higher expression of stress related proteins growing on both carbon sources. CONCLUSIONS It is obvious from the data obtained in this study that the proteomic approach efficiently identifies differentially expressed proteins caused by the change of carbon source. Despite the basic similarity in the strains metabolic routes when they ferment glucose and ribose, there were also interesting differences. From the application point of view, an understanding of regulatory mechanisms, actions of catabolic enzymes and proteins, and preference of carbon source is of great importance.
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Affiliation(s)
- Anette McLeod
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, NO-1430 Ås, Norway
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Monique Zagorec
- Unité Flore Lactique et Environnement Carné, UR309, INRA, Domaine de Vilvert, F-78350 Jouy en Josas, France
| | | | - Kristine Naterstad
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, NO-1430 Ås, Norway
| | - Lars Axelsson
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, NO-1430 Ås, Norway
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Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, Walter J. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME JOURNAL 2009; 4:377-87. [PMID: 19924154 DOI: 10.1038/ismej.2009.123] [Citation(s) in RCA: 191] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The vertebrate digestive tract, including that of humans, is the habitat to trillions of bacteria that are of significant importance to host biology and health. Although these communities are often postulated to have coevolved with their hosts, evidence is lacking, yet critical for our understanding of microbial symbiosis in vertebrates. To gain insight into the evolution of a gut symbiont, we have characterized the population genetic structure and phylogeny of Lactobacillus reuteri strains isolated from six different host species (human, mouse, rat, pig, chicken and turkey) using Amplified-Fragment Length Polymorphism (AFLP) and Multi-Locus Sequence Analysis (MLSA). The results revealed considerable genetic heterogeneity within the L. reuteri population and distinct monophyletic clades reflecting host origin but not provenance. The evolutionary patterns detected indicate a long-term association of L. reuteri lineages with particular vertebrate species and host-driven diversification. Results from a competition experiment in a gnotobiotic mouse model revealed that rodent isolates showed elevated ecological performance, indicating that evolution of L. reuteri lineages was adaptive. These findings provide evidence that some vertebrate gut microbes are not promiscuous, but have diversified into host-adapted lineages by a long-term evolutionary process, allowing the development of a highly specialized symbiosis.
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Affiliation(s)
- Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583-0919, USA
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Chiaramonte F, Blugeon S, Chaillou S, Langella P, Zagorec M. Behavior of the meat-borne bacterium Lactobacillus sakei during its transit through the gastrointestinal tracts of axenic and conventional mice. Appl Environ Microbiol 2009; 75:4498-505. [PMID: 19447958 PMCID: PMC2704804 DOI: 10.1128/aem.02868-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 05/06/2009] [Indexed: 11/20/2022] Open
Abstract
A Lactobacillus sakei strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne L. sakei strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three L. sakei strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10(9) CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total L. sakei population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that L. sakei is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of Escherichia coli strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.
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MESH Headings
- Animals
- Cluster Analysis
- Colony Count, Microbial
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Feces/microbiology
- Gastrointestinal Tract/microbiology
- Genes, Bacterial
- Humans
- Lactobacillus/genetics
- Lactobacillus/isolation & purification
- Lactobacillus/physiology
- Lactobacillus/ultrastructure
- Meat/microbiology
- Mice
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev 2009; 72:728-64, Table of Contents. [PMID: 19052326 DOI: 10.1128/mmbr.00017-08] [Citation(s) in RCA: 630] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lactobacilli have been crucial for the production of fermented products for centuries. They are also members of the mutualistic microbiota present in the human gastrointestinal and urogenital tract. Recently, increasing attention has been given to their probiotic, health-promoting capacities. Many human intervention studies demonstrating health effects have been published. However, as not all studies resulted in positive outcomes, scientific interest arose regarding the precise mechanisms of action of probiotics. Many reported mechanistic studies have addressed mainly the host responses, with less attention being focused on the specificities of the bacterial partners, notwithstanding the completion of Lactobacillus genome sequencing projects, and increasing possibilities of genomics-based and dedicated mutant analyses. In this emerging and highly interdisciplinary field, microbiologists are facing the challenge of molecular characterization of probiotic traits. This review addresses the advances in the understanding of the probiotic-host interaction with a focus on the molecular microbiology of lactobacilli. Insight into the molecules and genes involved should contribute to a more judicious application of probiotic lactobacilli and to improved screening of novel potential probiotics.
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Huys G, Vanhoutte T, Vandamme P. Application of sequence-dependent electrophoresis fingerprinting in exploring biodiversity and population dynamics of human intestinal microbiota: what can be revealed? Interdiscip Perspect Infect Dis 2008; 2008:597603. [PMID: 19277102 PMCID: PMC2648627 DOI: 10.1155/2008/597603] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 09/22/2008] [Indexed: 01/13/2023] Open
Abstract
Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of complex microbial ecosystems independent of their culturability and without prior knowledge on the complexity and diversity of the ecosystem. Mainly using the prokaryotic 16S rRNA gene as PCR amplification target, SDE-based community fingerprinting turned into one of the leading molecular tools to unravel the diversity and population dynamics of human intestinal microbiota. The first part of this review covers the methodological concept of SDE fingerprinting and the technical hurdles for analyzing intestinal samples. Subsequently, the current state-of-the-art of DGGE and related techniques to analyze human intestinal microbiota from healthy individuals and from patients with intestinal disorders is surveyed. In addition, the applicability of SDE analysis to monitor intestinal population changes upon nutritional or therapeutic interventions is critically evaluated.
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Affiliation(s)
- Geert Huys
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Tom Vanhoutte
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol 2008; 74:4985-96. [PMID: 18539818 DOI: 10.1128/aem.00753-08] [Citation(s) in RCA: 486] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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50
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The effects of fermented milks with simple and complex probiotic mixtures on the intestinal microbiota and immune response of healthy adults and children. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2007.01.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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