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Feng S, Guo Y, Wang Q, Meng M, Liu X, Zhang C, Zheng H, Guo H, Lu R, Li D, Su Z, Song H, Liang Y. UPLC/Q-TOF-MS-based metabolomics and molecular docking analysis of Bifidobacterium adolescentis exposure to levofloxacin. Biomed Chromatogr 2024; 38:e5862. [PMID: 38684194 DOI: 10.1002/bmc.5862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/04/2024] [Accepted: 02/26/2024] [Indexed: 05/02/2024]
Abstract
Antibiotic-associated diarrhea is a common adverse reaction caused by the widespread use of antibiotics. The decrease in probiotics is one of the reasons why antibiotics cause drug-induced diarrhea. However, few studies have addressed the intrinsic mechanism of antibiotics inhibiting probiotics. To investigate the underlying mechanism of levofloxacin against Bifidobacterium adolescentis, we used a metabolomics mass spectrometry-based approach and molecular docking analysis for a levofloxacin-induced B. adolescentis injury model. The results showed that levofloxacin reduced the survival rate of B. adolescentis and decreased the number of B. adolescentis. The untargeted metabolomics analysis identified 27 potential biomarkers, and many of these metabolites are involved in energy metabolism, amino acid metabolism and the lipid metabolism pathway. Molecular docking showed that levofloxacin can bind with aminoacyl-tRNA synthetase and lactic acid dehydrogenase. This result provides a novel insight into the mechanism of the adverse reactions of levofloxacin.
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Affiliation(s)
- Shisui Feng
- Pharmaceutical College, Guangxi Medical University, Nanning, China
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yue Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qianyi Wang
- Department of pharmacy, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Mingwei Meng
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Xi Liu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Chi Zhang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hua Zheng
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Hongwei Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Rigang Lu
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Danfeng Li
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Zhiheng Su
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hui Song
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yonghong Liang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
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2
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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3
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Walsh C, Owens RA, Bottacini F, Lane JA, van Sinderen D, Hickey RM. HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells. Front Microbiol 2023; 14:1232173. [PMID: 38163079 PMCID: PMC10757668 DOI: 10.3389/fmicb.2023.1232173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
The ability of gut commensals to adhere to the intestinal epithelium can play a key role in influencing the composition of the gut microbiota. Bifidobacteria are associated with a multitude of health benefits and are one of the most widely used probiotics for humans. Enhanced bifidobacterial adhesion may increase host-microbe, microbe-nutrient, and/or microbe-microbe interactions, thereby enabling consolidated health benefits to the host. The objective of this study was to determine the ability of human milk oligosaccharides (HMOs) to enhance bifidobacterial intestinal adhesion in vitro. This study assessed the colonisation-promoting effects of HMOs on four commercial infant-associated Bifidobacterium strains (two B. longum subsp. infantis strains, B. breve and B. bifidum). HT29-MTX cells were used as an in vitro intestinal model for bacterial adhesion. Short-term exposure of four commercial infant-associated Bifidobacterium strains to HMOs derived from breastmilk substantially increased the adherence (up to 47%) of these probiotic strains. Interestingly, when strains were incubated with HMOs as a four-strain combination, the number of viable bacteria adhering to intestinal cells increased by >90%. Proteomic analysis of this multi-strain bifidobacterial mixture revealed that the increased adherence resulting from exposure to HMOs was associated with notable increases in the abundance of sortase-dependent pili and glycosyl hydrolases matched to Bifidobacterium bifidum. This study suggests that HMOs may prime infant gut-associated Bifidobacterium for colonisation to intestinal epithelial cells by influencing the expression of various colonization factors.
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Affiliation(s)
- Clodagh Walsh
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- Health and Happiness Group, H&H Research, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesca Bottacini
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
- Biological Sciences and ADAPT Research Centre, Munster Technological University, Cork, Ireland
| | | | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Rita M. Hickey
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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4
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Mejia ME, Mercado-Evans V, Zulk JJ, Ottinger S, Ruiz K, Ballard MB, Fowler SW, Britton RA, Patras KA. Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model. NPJ Biofilms Microbiomes 2023; 9:87. [PMID: 37985659 PMCID: PMC10661851 DOI: 10.1038/s41522-023-00454-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (HMbmice). Like the community structure in conventional mice, HMbmice vaginal microbiota clustered into community state types but, uniquely, HMbmice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, HMbmice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous HMbmouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, HMbmice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.
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Affiliation(s)
- Marlyd E Mejia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Vicki Mercado-Evans
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Ottinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Korinna Ruiz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mallory B Ballard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie W Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Kathryn A Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA.
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5
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Suzuki S, Yokota K, Igimi S, Kajikawa A. Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances. Sci Rep 2023; 13:15632. [PMID: 37730901 PMCID: PMC10511705 DOI: 10.1038/s41598-023-42840-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Ligilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1-mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.
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Affiliation(s)
- Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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6
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Molina MA, Melchers WJ, Andralojc KM, Leenders WP, Huynen MA. Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection. Comput Struct Biotechnol J 2023; 21:4424-4431. [PMID: 37731597 PMCID: PMC10507478 DOI: 10.1016/j.csbj.2023.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.
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Affiliation(s)
- Mariano A. Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Willem J.G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands
| | - Karolina M. Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands
| | | | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, the Netherlands
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7
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Pardo-Esté C, Leiva SG, Remonsellez F, Castro-Nallar E, Castro-Severyn J, Saavedra CP. Exploring the Influence of Small-Scale Geographical and Seasonal Variations Over the Microbial Diversity in a Poly-extreme Athalosaline Wetland. Curr Microbiol 2023; 80:297. [PMID: 37490160 PMCID: PMC10368551 DOI: 10.1007/s00284-023-03395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023]
Abstract
Microorganisms are the most diverse life form on the planet and are critical for maintaining the geochemical cycles, especially in extreme environments. Bacterial communities are dynamic and respond directly to changes in abiotic conditions; among these communities, poly-extremophiles are particularly sensitive to perturbations due to their high specialization. Salar de Huasco is a high-altitude wetland located on the Chilean Altiplano exhibiting several conditions considered extreme for life, including negative water balance, extreme variations in temperature and pH values, high UV radiation, and the presence of various toxic metal(oids). However, previous reports have revealed a diverse bacterial community that has adapted to these conditions, here, we aimed to determine whether microbial community diversity and composition changed in response to geographical and seasonal variations. We found that there are significant differences in diversity, abundance, and composition in bacterial taxa that could be attributed to local geographical and seasonal variations, which in turn, can be associated with microbial traits. In conclusion, in this poly-extreme environment, small-scale changes can trigger significant changes in the microbial communities that maintain basic biogeochemical cycles. Further in depth analysis of microbial functionality and geo-ecological dynamics are necessary to better understand the relationships between seasonal changes and bacterial communities.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - Sergio Guajardo Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile.
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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Jeon S, Hwang J, Do H, Le LTHL, Lee CW, Yoo W, Lee MJ, Shin SC, Kim KK, Kim HW, Lee JH. Feruloyl Esterase ( LaFae) from Lactobacillus acidophilus: Structural Insights and Functional Characterization for Application in Ferulic Acid Production. Int J Mol Sci 2023; 24:11170. [PMID: 37446348 DOI: 10.3390/ijms241311170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
Ferulic acid and related hydroxycinnamic acids, used as antioxidants and preservatives in the food, cosmetic, pharmaceutical and biotechnology industries, are among the most abundant phenolic compounds present in plant biomass. Identification of novel compounds that can produce ferulic acid and hydroxycinnamic acids, that are safe and can be mass-produced, is critical for the sustainability of these industries. In this study, we aimed to obtain and characterize a feruloyl esterase (LaFae) from Lactobacillus acidophilus. Our results demonstrated that LaFae reacts with ethyl ferulate and can be used to effectively produce ferulic acid from wheat bran, rice bran and corn stalks. In addition, xylanase supplementation was found to enhance LaFae enzymatic hydrolysis, thereby augmenting ferulic acid production. To further investigate the active site configuration of LaFae, crystal structures of unliganded and ethyl ferulate-bound LaFae were determined at 2.3 and 2.19 Å resolutions, respectively. Structural analysis shows that a Phe34 residue, located at the active site entrance, acts as a gatekeeper residue and controls substrate binding. Mutating this Phe34 to Ala produced an approximately 1.6-fold increase in LaFae activity against p-nitrophenyl butyrate. Our results highlight the considerable application potential of LaFae to produce ferulic acid from plant biomass and agricultural by-products.
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Affiliation(s)
- Sangeun Jeon
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 07505, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 07505, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 07505, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 07505, Republic of Korea
| | - Ly Thi Huong Luu Le
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Chang Woo Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 07505, Republic of Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Min Ju Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 07505, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 07505, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 07505, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 07505, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 07505, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 07505, Republic of Korea
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9
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Spaggiari L, Squartini Ramos GB, Squartini Ramos CA, Ardizzoni A, Pedretti N, Blasi E, De Seta F, Pericolini E. Anti- Candida and Anti-Inflammatory Properties of a Vaginal Gel Formulation: Novel Data Concerning Vaginal Infection and Dysbiosis. Microorganisms 2023; 11:1551. [PMID: 37375053 DOI: 10.3390/microorganisms11061551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Vaginal ecosystem is a unique environment where, in physiological conditions, lactobacilli dominate. However, pathogenic microbial species responsible for vaginitis and vaginosis can also harbor vaginal microbiota. To extend our previously published data, we analyzed here both the anti-Candida and anti-inflammatory properties of the vaginal gel formulation, Respecta® Balance Gel (RBG), commercialized as an adjuvant to treat vaginitis and vaginosis. We evaluated its activity by an in vitro model where a monolayer of A-431 vaginal epithelial cells was infected by Candida albicans in the presence of RBG or the placebo formulation (pRBG). Specifically, we tested the RBG capacity to counteract C. albicans virulence factors and their anti-inflammatory properties. Our results show that, unlike the placebo, RBG reduces C. albicans adhesion, its capacity to form hyphae and C. albicans-induced vaginal cell damage. Interestingly, both RBG and pRBG reduce LPS-induced IL-8 secretion (with RBG being the most effective), demonstrating that also the placebo retains anti-inflammatory properties. From our experimental approach, we highlighted the possible role of farnesol on such effects, but we would like to point out that lactic acid, polydextrose and glycogen too must be relevant in the actual application. In summary, our results show that RBG impairs C. albicans virulence and is able to reduce the inflammation in the vaginal environment, ultimately allowing the establishment of a balanced vaginal ecosystem.
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Affiliation(s)
- Luca Spaggiari
- Clinical and Experimental Medicine Ph.D. Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Gianfranco B Squartini Ramos
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Caterina A Squartini Ramos
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Andrea Ardizzoni
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Natalia Pedretti
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elisabetta Blasi
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Francesco De Seta
- Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy
- Institute for Maternal and Child Health, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Burlo Garofolo, 34127 Trieste, Italy
| | - Eva Pericolini
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
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10
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Dukes HE, Tinker KA, Ottesen EA. Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics. Front Microbiol 2023; 14:1156809. [PMID: 37323917 PMCID: PMC10266427 DOI: 10.3389/fmicb.2023.1156809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
Omnivorous cockroaches host a complex hindgut microbiota comprised of insect-specific lineages related to those found in mammalian omnivores. Many of these organisms have few cultured representatives, thereby limiting our ability to infer the functional capabilities of these microbes. Here we present a unique reference set of 96 high-quality single cell-amplified genomes (SAGs) from bacterial and archaeal cockroach gut symbionts. We additionally generated cockroach hindgut metagenomic and metatranscriptomic sequence libraries and mapped them to our SAGs. By combining these datasets, we are able to perform an in-depth phylogenetic and functional analysis to evaluate the abundance and activities of the taxa in vivo. Recovered lineages include key genera within Bacteroidota, including polysaccharide-degrading taxa from the genera Bacteroides, Dysgonomonas, and Parabacteroides, as well as a group of unclassified insect-associated Bacteroidales. We also recovered a phylogenetically diverse set of Firmicutes exhibiting a wide range of metabolic capabilities, including-but not limited to-polysaccharide and polypeptide degradation. Other functional groups exhibiting high relative activity in the metatranscriptomic dataset include multiple putative sulfate reducers belonging to families in the Desulfobacterota phylum and two groups of methanogenic archaea. Together, this work provides a valuable reference set with new insights into the functional specializations of insect gut symbionts and frames future studies of cockroach hindgut metabolism.
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Affiliation(s)
- Helen E Dukes
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Kara A Tinker
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, United States
| | - Elizabeth A Ottesen
- Department of Microbiology, University of Georgia, Athens, GA, United States
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11
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Miao J, Regan J, Cai C, Palmer GE, Williams DL, Kruppa MD, Peters BM. Glycogen Metabolism in Candida albicans Impacts Fitness and Virulence during Vulvovaginal and Invasive Candidiasis. mBio 2023; 14:e0004623. [PMID: 36840583 PMCID: PMC10127583 DOI: 10.1128/mbio.00046-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
The polymorphic fungus Candida albicans remains a leading cause of both invasive and superficial mycoses, including vulvovaginal candidiasis (VVC). Metabolic plasticity, including carbohydrate catabolism, confers fitness advantages at anatomical site-specific host niches. C. albicans possesses the capacity to accumulate and store carbohydrates as glycogen and can consume intracellular glycogen stores when nutrients become limited. In the vaginal environment, estrogen promotes epithelial glycogen accumulation and C. albicans colonization. However, whether these factors are mechanistically linked is unexplored. Here, we characterized the glycogen metabolism pathways in C. albicans and investigated whether these impact the long-term survival of C. albicans, both in vitro and in vivo during murine VVC, or virulence during systemic infection. SC5314 and 6 clinical isolates demonstrated impaired growth when glycogen was used as the sole carbon source, suggesting that environmental glycogen acquisition is limited. The genetic deletion and complementation of key genes involved in glycogen metabolism in Saccharomyces cerevisiae confirmed that GSY1 and GLC3, as well as GPH1 and GDB1, are essential for glycogen synthesis and catabolism in C. albicans, respectively. Potential compensatory roles for a glucoamylase encoded by SGA1 were also explored. Competitive survival assays revealed that gsy1Δ/Δ, gph1Δ/Δ, and gph1Δ/Δ sga1Δ/Δ mutants exhibited long-term survival defects in vitro under starvation conditions and in vivo during vaginal colonization. A complete inability to catabolize glycogen (gph1Δ/Δ sga1Δ/Δ) also rendered C. albicans significantly less virulent during disseminated infections. This is the first study fully validating the glycogen metabolism pathways in C. albicans, and the results further suggest that intracellular glycogen catabolism positively impacts the long-term fitness of C. albicans in nutrient deficient environments and is important for full virulence. IMPORTANCE Glycogen is a highly branched polymer of glucose and is used across the tree of life as an efficient and compact form of energy storage. Whereas glycogen metabolism pathways have been studied in model yeasts, they have not been extensively explored in pathogenic fungi. Using a combination of microbiologic, molecular genetic, and biochemical approaches, we reveal orthologous functions of glycogen metabolism genes in the fungal pathogen Candida albicans. We also provide evidence that extracellular glycogen poorly supports growth across the Candida species and clinical isolates. Competitive fitness assays reveal that the loss of glycogen synthesis or catabolism significantly impacts survival during both in vitro starvation and the colonization of the mouse vagina. Moreover, a global glycogen catabolism mutant is rendered less virulent during murine invasive candidiasis. Therefore, this work demonstrates that glycogen metabolism in C. albicans contributes to survival and virulence in the mammalian host and may be a novel antifungal target.
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Affiliation(s)
- Jian Miao
- Pharmaceutical Sciences Program, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jessica Regan
- Pharmaceutical Sciences Program, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Chun Cai
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Glen E. Palmer
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - David L. Williams
- Department of Surgery, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
- Center of Excellence in Inflammation, Infectious Disease, and Immunity, East Tennessee State University, Johnson City, Tennessee, USA
| | - Michael D. Kruppa
- Center of Excellence in Inflammation, Infectious Disease, and Immunity, East Tennessee State University, Johnson City, Tennessee, USA
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Brian M. Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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12
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Esteban-Torres M, Ruiz L, Rossini V, Nally K, van Sinderen D. Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait. Gut Microbes 2023; 15:2235067. [PMID: 37526383 PMCID: PMC10395257 DOI: 10.1080/19490976.2023.2235067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.
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Affiliation(s)
- Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Benefitial Microbes (MicroHealth Group), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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13
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Journey of the Probiotic Bacteria: Survival of the Fittest. Microorganisms 2022; 11:microorganisms11010095. [PMID: 36677387 PMCID: PMC9861974 DOI: 10.3390/microorganisms11010095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
This review aims to bring a more general view of the technological and biological challenges regarding production and use of probiotic bacteria in promoting human health. After a brief description of the current concepts, the challenges for the production at an industrial level are presented from the physiology of the central metabolism to the ability to face the main forms of stress in the industrial process. Once produced, these cells are processed to be commercialized in suspension or dried forms or added to food matrices. At this stage, the maintenance of cell viability and vitality is of paramount for the quality of the product. Powder products requires the development of strategies that ensure the integrity of components and cellular functions that allow complete recovery of cells at the time of consumption. Finally, once consumed, probiotic cells must face a very powerful set of physicochemical mechanisms within the body, which include enzymes, antibacterial molecules and sudden changes in pH. Understanding the action of these agents and the induction of cellular tolerance mechanisms is fundamental for the selection of increasingly efficient strains in order to survive from production to colonization of the intestinal tract and to promote the desired health benefits.
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14
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Elokil AA, Chen W, Mahrose K, Elattrouny MM, Abouelezz KFM, Ahmad HI, Liu HZ, Elolimy AA, Mandouh MI, Abdelatty AM, Li S. Early life microbiota transplantation from highly feed-efficient broiler improved weight gain by reshaping the gut microbiota in laying chicken. Front Microbiol 2022; 13:1022783. [PMID: 36466637 PMCID: PMC9715608 DOI: 10.3389/fmicb.2022.1022783] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/10/2022] [Indexed: 08/27/2023] Open
Abstract
Starting phase of laying chicken life is the building stone for rearing and production stages. Since, fecal microbial transplantation (FMT) regulates the gut microbial diversity and affects the productive performance of the bird. The aim of this study is to evaluate the effect of FMT from feed-efficient broiler chicken could program the diversity of gut microbiota and growth of recipient native slow growing egg-laying chicks. For this, a total of 150 (one-day-old) Jing Hong chicks were randomly assigned into two groups, each group consisted of 5 replicates (n = 15 bird/ replicate). The control group (CON) and FMT recipient birds (FMT) fed on basal diet, the FMT group received an oral daily dose of FMT prepared from Cobb-500 chickens. The FMT performed from the 1d to 28d of age, through the experimental period, feed intake and body weight were recorded weekly. At the end of a 28-day trial, carcass traits were assessed and cecal samples were collected for microbiome assessment via 16S rRNA-based metagenomic analysis to characterize the diversity and functions of microbial communities. The data were statistically analyzed using R software. Body weight and body weight gain increased, and FCR decreased (p = 0.01) in FMT group. The relative abundance of Firmicutes and the Firmicutes/Bacteroidetes (F/B) ratio were increased due to FMT administration (p = 0.01). A higher relative abundance of Lactobacillus, Lactococcus, and Bifidobacterium were presented in the FMT group. Meanwhile, Enterococcus, Helicobacter, and Bacteroides were more abundant in the CON group (p < 0.01). Kyoto encyclopedia of genes and genomes (KEGG) pathways for microbial functions regarding amino acid metabolism, secondary metabolites biosynthesis, carbohydrate metabolism, energy metabolism, and enzyme families, cofactors, and vitamins were significantly annotated in the FMT group. Overall, FMT administration from the donor of highly feed-efficient broilers improved weight gain by reshaping a distinct gut microbiome, which may be related to the metabolism and health in the recipients laying chicks, providing new insight on the application of the FMT technique for early life programming of laying chickens.
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Affiliation(s)
- Abdelmotaleb A. Elokil
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Animal Production Department, Faculty of Agriculture, Moshtohor, Benha University, Mushthar, Egypt
| | - Wei Chen
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Key Laboratory of Poultry Genetics and Breeding, Ministry of Agriculture, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou, China
| | - Khalid Mahrose
- Animal and Poultry Production Department, Faculty of Technology and Development, Zagazig University, Zagazig, Egypt
| | - Mahmoud M. Elattrouny
- Animal Production Department, Faculty of Agriculture, Moshtohor, Benha University, Mushthar, Egypt
| | - Khaled F. M. Abouelezz
- Department of Poultry Production, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hua-Zhen Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ahmed A. Elolimy
- Department of Animal Production, National Research Centre, Giza, Egypt
| | - Mahmoud I. Mandouh
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Alzahraa M. Abdelatty
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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15
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Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways. Microorganisms 2022; 10:microorganisms10081637. [PMID: 36014054 PMCID: PMC9415760 DOI: 10.3390/microorganisms10081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.
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16
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Comparative transcriptome analysis reveals the contribution of membrane transporters to acid tolerance in Lactococcus lactis. J Biotechnol 2022; 357:9-17. [PMID: 35963594 DOI: 10.1016/j.jbiotec.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/08/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022]
Abstract
Acid stress caused by the accumulation of acidic metabolites severely affects the fermentation performance of lactic acid bacteria. In this study, to overcome the impact of acid stress during growth, nine membrane transporters were introduced in Lactococcus lactis NZ9000 to study their effects on acid tolerance. The engineered strains that overexpressed the metal ATP-binding cassette (ABC) transporters zitP (metal ABC transporter permease) and zitQ (metal ABC transporter ATP-binding protein) exhibited 14.5 and 9.5-fold higher survival rates, respectively, at pH 4.0 for 4 h than the control strain. During acid stress, the two recombinant strains maintained relatively higher ATP concentrations, i.e., 7.7- and 11.7-fold higher, respectively, than the control strain at pH 4.0 for 3 h. Subsequently, transcriptome analysis revealed that genes associated with ABC transporters, metal ion transport, transcriptional regulation, and stress response exhibited differentially expressed. The transcriptional level of ecfA2 gene (energy-coupling factor transporter ATPase) was substantially higher in L. lactis (ZitQ) during acid stress, and the ecfA2 gene was overexpressed in L. lactis. This recombinant strain L. lactis (EcfA2) exhibited a 598.7-fold higher survival rate than the control strain at pH 4.0 for 4 h. This study showed that the membrane transporters ZitP and ZitQ could increase acid tolerance and provided a strategy for constructing robust strains that can be used in food industry.
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17
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Wen ZT, Huang X, Ellepola K, Liao S, Li Y. Lactobacilli and human dental caries: more than mechanical retention. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35671222 DOI: 10.1099/mic.0.001196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactobacilli have been considered as major contributors to human dental caries for over a century. Recent in vitro model studies have shown that when compared to Streptococcus mutans, a keystone pathogen of human dental caries, the ability of lactobacilli to form biofilms is poor, although differences exist between the different major species. Further studies using molecular and bioinformatics approaches provide evidence that multiple mechanisms, including adhesin-receptor mediated physical contact with S. mutans, facilitate the adherence and establishment of lactobacilli on the tooth surface. There is also evidence that under conditions like continuous sugar consumption, weak acids and other antimicrobials such as bacteriocins from lactobacilli can become detrimental to the microbial community, especially those in the proximity. Details on the underlying mechanisms of how different Lactobacillus sp. establish and persist in the highly complex microbiota on the tooth surface await further investigation.
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Affiliation(s)
- Zezhang T Wen
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Xiaochang Huang
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Present address: Analysis and Testing Center, Nanchang University, 235 Nanjing East Load, Qingshan Lake District, Nanchang, PR China
| | - Kassapa Ellepola
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Present address: Department of Oral Biology, College of Dentistry, University of Illinois Chicago, Chicago, IL, USA
| | - Sumei Liao
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Yihong Li
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornel University, Ithaca, NY, USA
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18
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Shi J, Xia C, Tian Q, Zeng X, Wu Z, Guo Y, Pan D. Untargeted metabolomics based on LC–MS to elucidate the mechanism underlying nitrite degradation by Limosilactobacillus fermentum RC4. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Sałański P, Kowalczyk M, Bardowski JK, Szczepankowska AK. Health-Promoting Nature of Lactococcus lactis IBB109 and Lactococcus lactis IBB417 Strains Exhibiting Proliferation Inhibition and Stimulation of Interleukin-18 Expression in Colorectal Cancer Cells. Front Microbiol 2022; 13:822912. [PMID: 35694291 PMCID: PMC9174673 DOI: 10.3389/fmicb.2022.822912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/29/2022] [Indexed: 12/19/2022] Open
Abstract
Lactic acid bacteria (LAB) are Gram-positive bacteria which are considered for use as adjuvant therapeutics in management of various disease ailments, including obesity, irritable bowel syndrome, lactose intolerance and cancer. To investigate the possible use of Lactococcus lactis strains from our collection in treatment of gastrointestinal cancer, we tested them for the ability to arrest proliferation of human colorectal adenocarcinoma cells (Caco-2). Results of the BrdU assay showed that the anti-proliferative activity of L. lactis cells is strain-specific. We found that particularly, two strains, L. lactis IBB109 and L. lactis IBB417, exhibited the most potent inhibitory effect. Moreover, both strains triggered interleukin 18 gene expression, normally inhibited in Caco-2 (cancer) cells. To examine the probiotic potential of the two strains, we tested them for bile salts and acid tolerance, as well as adhesion properties. Both isolates exhibited probiotic potential—they survived in the presence of 0.3% bile salts and tolerated exposure to low pH and osmotic stress. Notably, we found that L. lactis IBB417 displayed better adherence to mucus and Caco-2 cells than L. lactis IBB109. Additionally, by microdilution tests we confirmed that both strains are sensitive to all nine antibiotics of human and veterinary importance listed by the European Food Safety Authority. Finally, by in silico investigations of whole genome sequencing data, we revealed the genetic features of L. lactis IBB109 and L. lactis IBB417 that can be associated with functional (e.g., adhesion and carbohydrate metabolic genes) and safety (e.g., virulence and antibiotic resistance) aspects of the strains, confirming their health-promoting potential.
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20
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Werum V, Ehrmann M, Vogel R, Hilgarth M. Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat. Microbiol Res 2022; 258:126982. [DOI: 10.1016/j.micres.2022.126982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
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21
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Son S, Lee R, Park SM, Lee SH, Lee HK, Kim Y, Shin D. Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:1411-1422. [PMID: 34957454 PMCID: PMC8672248 DOI: 10.5187/jast.2021.e126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/22/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022]
Abstract
Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.
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Affiliation(s)
- Seungwoo Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
| | - Raham Lee
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Jeonbuk National University, Jeonju 54896, Korea
| | - Seung-Moon Park
- Department of Bioenvironmental Chemistry, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Korea
| | | | - Hak-Kyo Lee
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea.,Department of Animal Biotechnology, College of Agricultural and Life Sciences, Jeonbuk National University, Jeonju 54896, Korea
| | - Yangseon Kim
- Center for Industrialization of Agriculture and Livestock Microorganism, Jeongeup 56212, Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
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22
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Dynamics of physiological responses of potentially probiotic fruit-derived Limosilactobacillus fermentum in apple and orange juices during refrigeration storage and exposure to simulated gastrointestinal conditions. Arch Microbiol 2021; 204:38. [DOI: 10.1007/s00203-021-02672-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022]
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23
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Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
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Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
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24
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Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization. Proc Natl Acad Sci U S A 2021; 118:2017709118. [PMID: 33526676 PMCID: PMC8017965 DOI: 10.1073/pnas.2017709118] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The transformation of bile acids (BAs) by the gut microbiota is increasingly recognized as an important factor shaping host health. The prerequisite step of BA metabolism is carried out by bile salt hydrolases (BSHs), which are encoded by select gut and probiotic bacteria. Despite their prevalence, the utility of harboring a bsh is unclear. Here, we investigate the role of BSHs encoded by Lactobacillus acidophilus and Lactobacillus gasseri. We show that BA type and BSH substrate preferences affect in vitro and in vivo growth of both species. These findings contribute to a mechanistic understanding of bacterial survival in various BA-rich niches and inform future efforts to leverage BSHs as a therapeutic tool for manipulating the gut microbiota. Primary bile acids (BAs) are a collection of host-synthesized metabolites that shape physiology and metabolism. BAs transit the gastrointestinal tract and are subjected to a variety of chemical transformations encoded by indigenous bacteria. The resulting microbiota-derived BA pool is a mediator of host–microbiota interactions. Bacterial bile salt hydrolases (BSHs) cleave the conjugated glycine or taurine from BAs, an essential upstream step for the production of deconjugated and secondary BAs. Probiotic lactobacilli harbor a considerable number and diversity of BSHs; however, their contribution to Lactobacillus fitness and colonization remains poorly understood. Here, we define and compare the functions of multiple BSHs encoded by Lactobacillus acidophilus and Lactobacillus gasseri. Our genetic and biochemical characterization of lactobacilli BSHs lend to a model of Lactobacillus adaptation to the gut. These findings deviate from previous notions that BSHs generally promote colonization and detoxify bile. Rather, we show that BSH enzymatic preferences and the intrinsic chemical features of various BAs determine the toxicity of these molecules during Lactobacillus growth. BSHs were able to alter the Lactobacillus transcriptome in a BA-dependent manner. Finally, BSHs were able to dictate differences in bacterial competition in vitro and in vivo, defining their impact on BSH-encoding bacteria within the greater gastrointestinal tract ecosystem. This work emphasizes the importance of considering the enzymatic preferences of BSHs alongside the conjugated/deconjugated BA–bacterial interaction. These results deepen our understanding of the BA–microbiome axis and provide a framework to engineer lactobacilli with improved bile resistance and use probiotics as BA-altering therapeutics.
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Han SR, Kim B, Jang JH, Park H, Oh TJ. Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. BMC Genomics 2021; 22:403. [PMID: 34078272 PMCID: PMC8171050 DOI: 10.1186/s12864-021-07734-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. RESULTS Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. CONCLUSIONS We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.
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Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Jong Hwa Jang
- Department of Dental Hygiene, College of Health Science, Dankook University, 119 Dandae-ro, Dongnam-gu, 31116, Cheonan-si, Chungnam, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, 02841, Seoul, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea.
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Sueda R, Yoshida K, Onodera M, Fukui T, Yatsunami R, Nakamura S. Characterization of a GlgC homolog from extremely halophilic archaeon Haloarcula japonica. Biosci Biotechnol Biochem 2021; 85:1441-1447. [PMID: 33749776 DOI: 10.1093/bbb/zbab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/16/2021] [Indexed: 11/12/2022]
Abstract
Glycogen synthesis in bacteria is mainly organized by the products of glgB, glgC, and glgA genes comprising the widely known glg operon. On the genome of extremely halophilic archaeon Haloarcula japonica, there was a gene cluster analogous to the bacterial glg operon. In this study, we focused on a GlgC homolog of Ha. japonica, and its recombinant enzyme was prepared and characterized. The enzyme showed highest activity toward GTP and glucose-1-phosphate as substrates in the presence of 2.6 m KCl and predicted to be work as "GDP-glucose pyrophosphorylase" in Ha. japonica.
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Affiliation(s)
- Rin Sueda
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Kento Yoshida
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Masahiko Onodera
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Rie Yatsunami
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.,National Institute of Technology, Numazu College, Numazu, Shizuoka, Japan
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Xiao Y, Zhai Q, Zhang H, Chen W, Hill C. Gut Colonization Mechanisms of Lactobacillus and Bifidobacterium: An Argument for Personalized Designs. Annu Rev Food Sci Technol 2021; 12:213-233. [DOI: 10.1146/annurev-food-061120-014739] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lactobacillus and Bifidobacterium spp. are best understood for their applications as probiotics, which are often transient, but as commensals it is probable that stable colonization in the gut is important for their beneficial roles. Recent research suggests that the establishment and persistence of strains of Lactobacillus and Bifidobacterium in the gut are species- and strain-specific and affected by natural history, genomic adaptability, and metabolic interactions of the bacteria and the microbiome and immune aspects of the host but also regulated by diet. This provides new perspectives on the underlying molecular mechanisms. With an emphasis on host–microbe interaction, this review outlines how the characteristics of individual Lactobacillus and Bifidobacterium bacteria, the host genotype and microbiome structure,diet, and host–microbe coadaptation during bacterial gut transition determine and influence the colonization process. The diet-tuned and personally tailored colonization can be achieved via a machine learning prediction model proposed here.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology and 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
- Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology and 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
- Beijing Advanced Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Colin Hill
- School of Microbiology and APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
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Bai DP, Lin XY, Hu YQ, Chen ZZ, Chen L, Huang YF, Huang XH, Li J. Metagenomics approach to identify lignocellulose-degrading enzymes in the gut microbiota of the Chinese bamboo rat cecum. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Wang C, Liu Q, Ye F, Tang H, Xiong Y, Wu Y, Wang L, Feng X, Zhang S, Wan Y, Huang J. Dietary purslane (Portulaca oleracea L.) promotes the growth performance of broilers by modulation of gut microbiota. AMB Express 2021; 11:31. [PMID: 33620605 PMCID: PMC7902751 DOI: 10.1186/s13568-021-01190-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/08/2021] [Indexed: 12/28/2022] Open
Abstract
Purslane is a widespread wild vegetable with both medicinal and edible properties. It is highly appreciated for its high nutritional value and is also considered as a high-quality feed resource for livestock and poultry. In this study, Sanhuang broilers were used to investigate the effect of feeding purslane diets on the growth performance in broilers and their gut microbiota. A total of 48 birds with good growth and uniform weight were selected and randomly allocated to four treatment groups A (control), B, C and D. Dietary treatments were fed with basal diet without purslane and diets containing 1%, 2% and 3% purslane. The 16S rDNA was amplified by PCR and sequenced using the Illumina HiSeq platform to analyze the composition and diversity of gut microbiota in the four sets of samples. The results showed that dietary inclusion of 2% and 3% purslane could significantly improve the growth performance and reduce the feed conversion ratio. Microbial diversity analysis indicated that the composition of gut microbiota of Sanhuang broilers mainly included Gallibacterium, Bacteroides and Escherichia-Shigella, etc. As the content of purslane was increased, the abundance of Lactobacillus increased significantly, and Escherichia-Shigella decreased. LEfSe analysis revealed that Bacteroides_caecigallinarum, Lachnospiraceae, Lactobacillales and Firmicutes had significant differences compared with the control group. PICRUSt analysis revealed bacteria mainly enriched in carbohydrate metabolism pathway due to the additon of purslane in the diet. These results suggest that the addition of purslane to feed could increase the abundance of Lactobacillus in intestine, modulate the environment of gut microbiota and promote the metabolism of carbohydrates to improve its growth performance. This study indicates that the effect of purslane on the growth-promoting performance of broilers might depend on its modulation on gut microbiota, so as to provide a certain scientific basis for the application of purslane in the feed industry.
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In Vivo Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression. mBio 2021; 12:mBio.03399-20. [PMID: 33500337 PMCID: PMC7858073 DOI: 10.1128/mbio.03399-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lactobacillus acidophilus NCFM is a probiotic strain commonly used in dairy products and dietary supplements. Postgenome in vitro studies of NCFM thus far have linked potential key genotypes to its probiotic-relevant attributes, including gut survival, prebiotic utilization, host interactions, and immunomodulatory activities. To corroborate and extend beyond previous in vivo and in vitro functional studies, we employed a dual RNA sequencing (RNA-seq) transcriptomic approach to identify genes potentially driving the gut fitness and activities of L. acidophilus NCFM in vivo, and in parallel, examine the ileal transcriptional response of its murine hosts during monocolonization. Spatial expression profiling of NCFM from the ileum through the colon revealed a set of 134 core genes that were consistently overexpressed during gut transit. These in vivo core genes are predominantly involved in the metabolism of carbohydrates, amino acids, and nucleotides, along with mucus-binding proteins and adhesion factors, confirming their functionally important roles in nutrient acquisition and gut retention. Functional characterization of the highly expressed major S-layer-encoding gene established its indispensable role as a cell shape determinant and maintenance of cell surface integrity, essential for viability and probiotic attributes. Host colonization by L. acidophilus resulted in significant downregulation of several proinflammatory cytokines and tight junction proteins. Genes related to redox signaling, mucin glycosylation, and circadian rhythm modulation were induced, suggesting impacts on intestinal development and immune functions. Metagenomic analysis of NCFM populations postcolonization demonstrated the genomic stability of L. acidophilus as a gut transient and further established its safety as a probiotic and biotherapeutic delivery platform.IMPORTANCE To date, our basis for comprehending the probiotic mechanisms of Lactobacillus acidophilus, one of the most widely consumed probiotic microbes, was largely limited to in vitro functional genomic studies. Using a germfree murine colonization model, in vivo-based transcriptional studies provided the first view of how L. acidophilus survives in the mammalian gut environment, including gene expression patterns linked to survival, efficient nutrient acquisition, stress adaptation, and host interactions. Examination of the host ileal transcriptional response, the primary effector site of L. acidophilus, has also shed light into the mechanistic roles of this probiotic microbe in promoting anti-inflammatory responses, maintaining intestinal epithelial homeostasis and modulation of the circadian-metabolic axis in its host.
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Physiological and Molecular Responses to Main Environmental Stressors of Microalgae and Bacteria in Polar Marine Environments. Microorganisms 2020; 8:microorganisms8121957. [PMID: 33317109 PMCID: PMC7764121 DOI: 10.3390/microorganisms8121957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/18/2022] Open
Abstract
The Arctic and Antarctic regions constitute 14% of the total biosphere. Although they differ in their physiographic characteristics, both are strongly affected by snow and ice cover changes, extreme photoperiods and low temperatures, and are still largely unexplored compared to more accessible sites. This review focuses on microalgae and bacteria from polar marine environments and, in particular, on their physiological and molecular responses to harsh environmental conditions. The data reported in this manuscript show that exposure to cold, increase in CO2 concentration and salinity, high/low light, and/or combination of stressors induce variations in species abundance and distribution for both polar bacteria and microalgae, as well as changes in growth rate and increase in cryoprotective compounds. The use of -omics techniques also allowed to identify specific gene losses and gains which could have contributed to polar environmental adaptation, and metabolic shifts, especially related to lipid metabolism and defence systems, such as the up-regulation of ice binding proteins, chaperones and antioxidant enzymes. However, this review also provides evidence that -omics resources for polar species are still few and several sequences still have unknown functions, highlighting the need to further explore polar environments, the biology and ecology of the inhabiting bacteria and microalgae, and their interactions.
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Patrone V, Al-Surrayai T, Romaniello F, Fontana A, Milani G, Sagheddu V, Puglisi E, Callegari ML, Al-Mansour H, Kishk MW, Morelli L. Integrated Phenotypic-Genotypic Analysis of Candidate Probiotic Weissella Cibaria Strains Isolated from Dairy Cows in Kuwait. Probiotics Antimicrob Proteins 2020; 13:809-823. [PMID: 33085038 PMCID: PMC8203532 DOI: 10.1007/s12602-020-09715-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 12/12/2022]
Abstract
Probiotics represent a possible strategy for controlling intestinal infections in livestock. Members of the Weissella genus are increasingly being studied for health-related applications in animals and humans. Here we investigated the functional properties of two Weissella cibaria strains isolated from cows reared in Kuwait breeding facilities by combining phenotypic with genomic analyses. W. cibaria SP7 and SP19 exhibited good growth in vitro under acidic conditions and in the presence of bile salts compared to the reference probiotic Lacticaseibacillus (formerly Lactobacillus) rhamnosus GG. Both strains were able to adhere to Caco-2 and HT-29 cell lines, as well as to mucin. The cell-free supernatants of the two isolates exhibited inhibitory activity towards Escherichia coli ATCC 25,922 and Salmonella enterica UC3605, which was ultimately due to the low pH of supernatants. W. cibaria SP19 showed a co-aggregation ability similar to that of L. rhamnosus GG when incubated with S. enterica. Whole genome sequencing and analysis revealed that both strains harbored several genes involved in carbohydrate metabolism and general stress responses, indicating bacterial adaptation to the gastrointestinal environment. We also detected genes involved in the adhesion to host epithelial cells or extracellular matrix. No evidence of acquired antibiotic resistance or hemolytic activity was found in either strain. These findings shed light on the potential of W. cibaria for probiotic use in livestock and on the mechanisms underlying host-microbe interaction in the gut. W. cibaria` strain SP19 exhibited the best combination of in vitro probiotic properties and genetic markers, and is a promising candidate for further investigation.
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Affiliation(s)
- Vania Patrone
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via E. Parmense 84, 29122, Piacenza, Italy
| | | | - Francesco Romaniello
- Biotechnological Research Centre, Università Cattolica del Sacro Cuore, via Milano 24, 26100, Cremona, Italy
| | - Alessandra Fontana
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via E. Parmense 84, 29122, Piacenza, Italy
| | - Giovanni Milani
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via E. Parmense 84, 29122, Piacenza, Italy
| | - Valeria Sagheddu
- AAT - Advanced Analytical Technologies Srl, Via P. Majavacca 12, 29107, Fiorenzuola d'Arda (Piacenza), Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via E. Parmense 84, 29122, Piacenza, Italy
| | - Maria Luisa Callegari
- Biotechnological Research Centre, Università Cattolica del Sacro Cuore, via Milano 24, 26100, Cremona, Italy.
| | | | | | - Lorenzo Morelli
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via E. Parmense 84, 29122, Piacenza, Italy
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Zhen N, Zeng X, Wang H, Yu J, Pan D, Wu Z, Guo Y. Effects of heat shock treatment on the survival rate of Lactobacillus acidophilus after freeze-drying. Food Res Int 2020; 136:109507. [DOI: 10.1016/j.foodres.2020.109507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 02/06/2023]
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Wang M, Liu Q, Kang X, Zhu Z, Yang H, Xi X, Zhang X, Du Y, Guo M, Tang D, Wang L. Glycogen Metabolism Impairment via Single Gene Mutation in the glgBXCAP Operon Alters the Survival Rate of Escherichia coli Under Various Environmental Stresses. Front Microbiol 2020; 11:588099. [PMID: 33101261 PMCID: PMC7546213 DOI: 10.3389/fmicb.2020.588099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Glycogen is a highly branched polysaccharide that is widely present in all life domains. It has been identified in many bacterial species and functions as an important energy storage compound. In addition, it plays important roles in bacterial transmission, pathogenicity, and environmental viability. There are five essential enzymes (coding genes) directly involved in bacterial glycogen metabolism, which forms a single operon glgBXCAP with a suboperonic promoter in glgC gene in Escherichia coli. Currently, there is no comparative study of how the disruptions of the five glycogen metabolism genes influence bacterial phenotypes, such as growth rate, biofilm formation, and environmental survival, etc. In this study, we systematically and comparatively studied five E. coli single-gene mutants (ΔglgC, ΔglgA, ΔglgB, ΔglgP, ΔglgX) in terms of glycogen metabolism and explored their phenotype changes with a focus on environmental stress endurance, such as nutrient deprivation, low temperature, desiccation, and oxidation, etc. Biofilm formation in wild-type and mutant strains was also compared. E. coli wild-type stores the highest glycogen content after around 20-h culture while disruption of degradation genes (glgP, glgX) leads to continuous accumulation of glycogen. However, glycogen primary structure was abnormally changed in ΔglgP and ΔglgX. Meanwhile, increased accumulation of glycogen facilitates the growth of E. coli mutants but reduces glucose consumption in liquid culture and vice versa. Glycogen metabolism disruption also significantly and consistently increases biofilm formation in all the mutants. As for environmental stress endurance, glycogen over-accumulating mutants have enhanced starvation viability and reduced desiccation viability while all mutants showed decreased survival rate at low temperature. No consistent results were found for oxidative stress resistance in terms of glycogen metabolism disruptions, though ΔglgA shows highest resistance toward oxidation with unknown mechanisms. In sum, single gene disruptions in glgBXCAP operon significantly influence bacterial growth and glucose consumption during culture. Accumulation and structure of intracellular glycogen were also significantly altered. In addition, we observed significant changes in E. coli environmental viabilities due to the deletions of certain genes in the operon. Further investigations shall be focused on the molecular mechanisms behind these phenotype changes.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Xingxing Kang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Sciences, Xuzhou Medical University, Xuzhou, China
| | - Huan Yang
- School of Laboratory Medicine, Xuzhou Medical University, Xuzhou, China
| | - Xiangyu Xi
- Xuzhou Infectious Disease Hospital, Xuzhou, China
| | - Xiao Zhang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Yan Du
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Liang Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
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An 1,4-α-Glucosyltransferase Defines a New Maltodextrin Catabolism Scheme in Lactobacillus acidophilus. Appl Environ Microbiol 2020; 86:AEM.00661-20. [PMID: 32444471 DOI: 10.1128/aem.00661-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022] Open
Abstract
The maltooligosaccharide (MOS) utilization locus in Lactobacillus acidophilus NCFM, a model for human small-intestine lactobacilli, encodes three glycoside hydrolases (GHs): a putative maltogenic α-amylase of family 13, subfamily 20 (LaGH13_20), a maltose phosphorylase of GH65 (LaGH65), and a family 13, subfamily 31, member (LaGH13_31B), annotated as a 1,6-α-glucosidase. Here, we reveal that LaGH13_31B is a 1,4-α-glucosyltransferase that disproportionates MOS with a degree of polymerization of ≥2, with a preference for maltotriose. Kinetic analyses of the three GHs encoded by the MOS locus revealed that the substrate preference of LaGH13_31B toward maltotriose complements the ~40-fold lower k cat of LaGH13_20 toward this substrate, thereby enhancing the conversion of odd-numbered MOS to maltose. The concerted action of LaGH13_20 and LaGH13_31B confers the efficient conversion of MOS to maltose that is phosphorolyzed by LaGH65. Structural analyses revealed the presence of a flexible elongated loop that is unique for a previously unexplored clade of GH13_31, represented by LaGH13_31B. The identified loop insertion harbors a conserved aromatic residue that modulates the activity and substrate affinity of the enzyme, thereby offering a functional signature of this clade, which segregates from 1,6-α-glucosidases and sucrose isomerases previously described within GH13_31. Genomic analyses revealed that the LaGH13_31B gene is conserved in the MOS utilization loci of lactobacilli, including acidophilus cluster members that dominate the human small intestine.IMPORTANCE The degradation of starch in the small intestine generates short linear and branched α-glucans. The latter are poorly digestible by humans, rendering them available to the gut microbiota, e.g., lactobacilli adapted to the small intestine and considered beneficial to health. This study unveils a previously unknown scheme of maltooligosaccharide (MOS) catabolism via the concerted activity of an 1,4-α-glucosyltransferase together with a classical hydrolase and a phosphorylase. The intriguing involvement of a glucosyltransferase likely allows the fine-tuning of the regulation of MOS catabolism for optimal harnessing of this key metabolic resource in the human small intestine. The study extends the suite of specificities that have been identified in GH13_31 and highlights amino acid signatures underpinning the evolution of 1,4-α-glucosyl transferases that have been recruited in the MOS catabolism pathway in lactobacilli.
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Lee MC, Hsu YJ, Ho HH, Hsieh SH, Kuo YW, Sung HC, Huang CC. Lactobacillus salivarius Subspecies salicinius SA-03 is a New Probiotic Capable of Enhancing Exercise Performance and Decreasing Fatigue. Microorganisms 2020; 8:microorganisms8040545. [PMID: 32283729 PMCID: PMC7232535 DOI: 10.3390/microorganisms8040545] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/23/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Probiotics are increasingly being used as a nutritional supplement by athletes to improve exercise performance and reduce post-exercise fatigue. Lactobacillus salivarius is a natural flora in the gastrointestinal tract of humans and animals. Lactobacillus salivarius subspecies salicinius (SA-03) is an isolate from the 2008 Olympic women’s 48 kg weightlifting gold medalist’s gut microbiota. In this study, we investigated its beneficial effects on physical fitness. Male ICR mice were divided into four groups (n = 10 per group) and orally administered with SA-03 for 4 weeks at 0, 2.05 × 109, 4.10 × 109, or 1.03 × 1010 CFU/kg/day. Results showed that 4 weeks of SA-03 supplementation significantly improved muscle strength and endurance performance, increased hepatic and muscular glycogen storage, and decreased lactate, blood urea nitrogen (BUN), ammonia, and creatine kinase (CK) levels after exercise. These observations suggest that SA-03 could be used as a nutritional supplement to enhance exercise performance and reduce.
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Affiliation(s)
- Mon-Chien Lee
- Graduate Institute of Sports Science, National Taiwan Sport University, No. 250, Wenhua 1st Rd., Guishan District, Taoyuan City 33301, Taiwan; (M.-C.L.); (Y.-J.H.)
| | - Yi-Ju Hsu
- Graduate Institute of Sports Science, National Taiwan Sport University, No. 250, Wenhua 1st Rd., Guishan District, Taoyuan City 33301, Taiwan; (M.-C.L.); (Y.-J.H.)
| | - Hsieh-Hsun Ho
- Glac Biotech Co. Ltd., Tainan City 74442, Taiwan; (H.-H.H.); (S.-H.H.); (Y.-W.K.)
| | - Shih-Hung Hsieh
- Glac Biotech Co. Ltd., Tainan City 74442, Taiwan; (H.-H.H.); (S.-H.H.); (Y.-W.K.)
| | - Yi-Wei Kuo
- Glac Biotech Co. Ltd., Tainan City 74442, Taiwan; (H.-H.H.); (S.-H.H.); (Y.-W.K.)
| | - Hsin-Ching Sung
- Aesthetic Medical Center, Department of Dermatology, Chang Gung Memorial Hospital, Taoyuan 33301, Taiwan
- Department of Anatomy, College of Medicine, Chang Gung University, No. 259, Wenhua 1st Rd., Guishan Township, Taoyuan City, Taoyuan 33301, Taiwan
- Correspondence: (H.-C.S.); (C.-C.H.); Tel.: +886-3-211-8800 (ext. 5977) (H.-C.S.); +886-3-328-3201 (ext. 2409) (C.-C.H.)
| | - Chi-Chang Huang
- Graduate Institute of Sports Science, National Taiwan Sport University, No. 250, Wenhua 1st Rd., Guishan District, Taoyuan City 33301, Taiwan; (M.-C.L.); (Y.-J.H.)
- Correspondence: (H.-C.S.); (C.-C.H.); Tel.: +886-3-211-8800 (ext. 5977) (H.-C.S.); +886-3-328-3201 (ext. 2409) (C.-C.H.)
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37
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Wang X, Tang D, Wang W. Adaptation strategies of
Pseudomonas protegens
SN15‐2 to hyperosmotic growth environment. J Appl Microbiol 2020; 128:1720-1734. [DOI: 10.1111/jam.14582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- X. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - D. Tang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - W. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
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38
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Pan M, Hidalgo-Cantabrana C, Barrangou R. Host and body site-specific adaptation of Lactobacillus crispatus genomes. NAR Genom Bioinform 2020; 2:lqaa001. [PMID: 33575551 PMCID: PMC7671364 DOI: 10.1093/nargab/lqaa001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/13/2022] Open
Abstract
Lactobacillus crispatus is a common inhabitant of both healthy poultry gut and human vaginal tract, and the absence of this species has been associated with a higher risk of developing infectious diseases. In this study, we analyzed 105 L. crispatus genomes isolated from a variety of ecological niches, including the human vaginal tract, human gut, chicken gut and turkey gut, to shed light on the genetic and functional features that drive evolution and adaptation of this important species. We performed in silico analyses to identify the pan and core genomes of L. crispatus, and to reveal the genomic differences and similarities associated with their origins of isolation. Our results demonstrated that, although a significant portion of the genomic content is conserved, human and poultry L. crispatus isolates evolved to encompass different genomic features (e.g. carbohydrate usage, CRISPR-Cas immune systems, prophage occurrence) in order to thrive in different environmental niches. We also observed that chicken and turkey L. crispatus isolates can be differentiated based on their genomic information, suggesting significant differences may exist between these two poultry gut niches. These results provide insights into host and niche-specific adaptation patterns in species of human and animal importance.
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Affiliation(s)
- Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
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39
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Wang L, Wang M, Wise MJ, Liu Q, Yang T, Zhu Z, Li C, Tan X, Tang D, Wang W. Recent progress in the structure of glycogen serving as a durable energy reserve in bacteria. World J Microbiol Biotechnol 2020; 36:14. [PMID: 31897771 DOI: 10.1007/s11274-019-2795-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022]
Abstract
Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, 6009, Australia
- Computer Science and Software Engineering, Faculty of Engineering and Mathematical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Ting Yang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Science, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Chengcheng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinle Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Wei Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
- The First Affiliated Hospital, Medical College of Shantou University, Shantou, 515041, Guangdong, China
- School of Public Health, Taishan Medical University, Tai'an, 271000, Shandong, China
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40
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Han SR, Kim DW, Kim B, Chi YM, Kang S, Park H, Jung SH, Lee JH, Oh TJ. Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation. Microb Pathog 2019; 137:103759. [PMID: 31560973 DOI: 10.1016/j.micpath.2019.103759] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022]
Abstract
Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.
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Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Do Wan Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Young Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea; Genome-based BioIT Convergence Institute, Asan, South Korea; Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea.
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41
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Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain. Appl Microbiol Biotechnol 2019; 103:7617-7634. [PMID: 31359102 PMCID: PMC6717177 DOI: 10.1007/s00253-019-10010-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 01/04/2023]
Abstract
Various Lactobacillus paracasei strains are found in diverse environments, including dairy and plant materials and the intestinal tract of humans and animals, and are also used in the food industry or as probiotics. In this study, we have isolated a new strain L. paracasei subsp. paracasei IBB3423 from samples of raw cow milk collected in a citizen science project. IBB3423 showed some desired probiotic features such as high adhesion capacity and ability to metabolize inulin. Its complete genome sequence comprising the chromosome of 3,183,386 bp and two plasmids of 5986 bp and 51,211 bp was determined. In silico analysis revealed numerous genes encoding proteins involved in carbohydrate metabolism and of extracellular localization likely supporting interaction with host tissues. In vitro tests confirmed the high adhesion capacity of IBB3423 and showed that it even exceeds that of the highly adhesive L. rhamnosus GG. Curing of the larger plasmid indicated that the adhesive properties depend on the plasmid and thus could be determined by its pilus-encoding spaCBA genes.
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42
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Gaucher F, Bonnassie S, Rabah H, Marchand P, Blanc P, Jeantet R, Jan G. Review: Adaptation of Beneficial Propionibacteria, Lactobacilli, and Bifidobacteria Improves Tolerance Toward Technological and Digestive Stresses. Front Microbiol 2019; 10:841. [PMID: 31068918 PMCID: PMC6491719 DOI: 10.3389/fmicb.2019.00841] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 04/02/2019] [Indexed: 01/15/2023] Open
Abstract
This review deals with beneficial bacteria, with a focus on lactobacilli, propionibacteria, and bifidobacteria. As being recognized as beneficial bacteria, they are consumed as probiotics in various food products. Some may also be used as starters in food fermentation. In either case, these bacteria may be exposed to various environmental stresses during industrial production steps, including drying and storage, and during the digestion process. In accordance with their adaptation to harsh environmental conditions, they possess adaptation mechanisms, which can be induced by pretreatments. Adaptive mechanisms include accumulation of compatible solutes and of energy storage compounds, which can be largely modulated by the culture conditions. They also include the regulation of energy production pathways, as well as the modulation of the cell envelop, i.e., membrane, cell wall, surface layers, and exopolysaccharides. They finally lead to the overexpression of molecular chaperones and of stress-responsive proteases. Triggering these adaptive mechanisms can improve the resistance of beneficial bacteria toward technological and digestive stresses. This opens new perspectives for the improvement of industrial processes efficiency with regard to the survival of beneficial bacteria. However, this bibliographical survey evidenced that adaptive responses are strain-dependent, so that growth and adaptation should be optimized case-by-case.
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Affiliation(s)
- Floriane Gaucher
- STLO, Agrocampus Ouest, Institut National de la Recherche Agronomique, Paris, France
- Bioprox, Levallois-Perret, France
| | - Sylvie Bonnassie
- STLO, Agrocampus Ouest, Institut National de la Recherche Agronomique, Paris, France
- Science de la Vie et de la Terre, Université de Rennes 1, Rennes, France
| | - Houem Rabah
- STLO, Agrocampus Ouest, Institut National de la Recherche Agronomique, Paris, France
- Pôle Agronomique Ouest, Bba, Rennes, France
| | | | | | - Romain Jeantet
- STLO, Agrocampus Ouest, Institut National de la Recherche Agronomique, Paris, France
| | - Gwénaël Jan
- STLO, Agrocampus Ouest, Institut National de la Recherche Agronomique, Paris, France
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43
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Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli. Curr Opin Biotechnol 2019; 56:163-171. [DOI: 10.1016/j.copbio.2018.11.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022]
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44
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Abstract
The Klaenhammer group at North Carolina State University pioneered genomic applications in food microbiology and beneficial lactic acid bacteria used as starter cultures and probiotics. Dr. Todd Klaenhammer was honored to be the first food scientist elected to the National Academy of Sciences (2001). The program was recognized with the highest research awards presented by the American Dairy Science Association (Borden Award 1996), the Institute of Food Technologists (Nicholas Appert Medal, 2007), and the International Dairy Federation (Eli Metchnikoff Award in Biotechnology, 2010) as well as with the Outstanding Achievement Award from the University of Minnesota (2001) and the Oliver Max Gardner Award (2009) for outstanding research across the 16-campus University of North Carolina system. Dr. Klaenhammer is a fellow of the American Association for the Advancement of Science, the American Dairy Science Association, and the Institute of Food Technology. Over his career, six of his PhD graduate students were awarded the annual Kenneth Keller award for the outstanding PhD dissertation that year in the College of Agriculture and Life Sciences. He championed the use of basic microbiology and genomic approaches to set a platform for translational applications of beneficial microbes in foods and their use in food preservation and probiotics and as oral delivery vehicles for vaccines and biotherapeutics. Dr. Klaenhammer was also a founding and co-chief editor of the Annual Review of Food Science and Technology.
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Affiliation(s)
- Todd Robert Klaenhammer
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA;
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45
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Zeng X, Pan Q, Guo Y, Wu Z, Sun Y, Dang Y, Cao J, He J, Pan D. Potential mechanism of nitrite degradation by Lactobacillus fermentum RC4 based on proteomic analysis. J Proteomics 2019; 194:70-78. [DOI: 10.1016/j.jprot.2018.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023]
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46
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Complete genome sequences of a H2O2-resistant psychrophilic bacterium Colwellia sp. Arc7-D isolated from Arctic Ocean sediment. Mar Genomics 2019. [DOI: 10.1016/j.margen.2018.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Comparative genomic analysis of Lactobacillus mucosae LM1 identifies potential niche-specific genes and pathways for gastrointestinal adaptation. Genomics 2019; 111:24-33. [DOI: 10.1016/j.ygeno.2017.12.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 01/02/2023]
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48
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Tomar O. The effects of probiotic cultures on the organic acid content, texture profile and sensory attributes of Tulum cheese. INT J DAIRY TECHNOL 2018. [DOI: 10.1111/1471-0307.12574] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oktay Tomar
- Engineering Faculty Food Engineering Department Afyon Kocatepe University Afyonkarahisar 03200 Turkey
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49
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Huang S, Gaucher F, Cauty C, Jardin J, Le Loir Y, Jeantet R, Chen XD, Jan G. Growth in Hyper-Concentrated Sweet Whey Triggers Multi Stress Tolerance and Spray Drying Survival in Lactobacillus casei BL23: From the Molecular Basis to New Perspectives for Sustainable Probiotic Production. Front Microbiol 2018; 9:2548. [PMID: 30405593 PMCID: PMC6204390 DOI: 10.3389/fmicb.2018.02548] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei BL23 has a recognized probiotic potential, which includes immune modulation, protection toward induced colitis, toward induced colon cancer and toward dissemination of pathogens. In L. casei, as well as in other probiotics, both probiotic and technological abilities are highly dependent (1) on the substrate used to grow bacteria and (2) on the process used to dry and store this biomass. Production and storage of probiotics, at a reasonable financial and environmental cost, becomes a crucial challenge. Food-grade media must be used, and minimal process is preferred. In this context, we have developed a “2-in-1” medium used both to grow and to dry L. casei BL23, considered a fragile probiotic strain. This medium consists in hyper-concentrated sweet whey (HCSW). L. casei BL23 grows in HCSW up to 30% dry matter, which is 6 times-concentrated sweet whey. Compared to isotonic sweet whey (5% dry matter), these growth conditions enhanced tolerance of L. casei BL23 toward heat, acid and bile salts stress. HCSW also triggered intracellular accumulation of polyphosphate, of glycogen and of trehalose. A gel-free global proteomic differential analysis further evidenced overexpression of proteins involved in pathways known to participate in stress adaptation, including environmental signal transduction, oxidative and metal defense, DNA repair, protein turnover and repair, carbohydrate, phosphate and amino acid metabolism, and in osmoadaptation. Accordingly, HCSW cultures of L. casei BL23 exhibited enhanced survival upon spray drying, a process known to drastically affect bacterial viability. This work opens new perspectives for sustainable production of dried probiotic lactobacilli, using food industry by-products and lowering energy costs.
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Affiliation(s)
- Song Huang
- Suzhou Key Laboratory of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Jiangsu, China.,UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Floriane Gaucher
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France.,Bioprox, Levallois-Perret, France
| | - Chantal Cauty
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Julien Jardin
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Yves Le Loir
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Romain Jeantet
- Suzhou Key Laboratory of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Jiangsu, China.,UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Xiao Dong Chen
- Suzhou Key Laboratory of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Jiangsu, China
| | - Gwénaël Jan
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
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50
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Roenneke B, Rosenfeldt N, Derya SM, Novak JF, Marin K, Krämer R, Seibold GM. Production of the compatible solute α-D-glucosylglycerol by metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2018; 17:94. [PMID: 29908566 PMCID: PMC6004087 DOI: 10.1186/s12934-018-0939-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/05/2018] [Indexed: 01/01/2023] Open
Abstract
Background α-d-Glucosylglycerol (αGG) has beneficial functions as a moisturizing agent in cosmetics and potential as a health food material, and therapeutic agent. αGG serves as compatible solute in various halotolerant cyanobacteria such as Synechocystis sp. PCC 6803, which synthesizes αGG in a two-step reaction: The enzymatic condensation of ADP-glucose and glycerol 3-phosphate by GG-phosphate synthase (GGPS) is followed by the dephosphorylation of the intermediate by the GG-phosphate phosphatase (GGPP). The Gram-positive Corynebacterium glutamicum, an industrial workhorse for amino acid production, does not utilize αGG as a substrate and was therefore chosen for the development of a heterologous microbial production platform for αGG. Results Plasmid-bound expression of ggpS and ggpP from Synechocystis sp. PCC 6803 enabled αGG synthesis exclusively in osmotically stressed cells of C. glutamicum (pEKEx2-ggpSP), which is probably due to the unique intrinsic control mechanism of GGPS activity in response to intracellular ion concentrations. C. glutamicum was then engineered to optimize precursor supply for αGG production: The precursor for αGG synthesis ADP-glucose gets metabolized by both the glgA encoded glycogen synthase and the otsA encoded trehalose-6-phosphate synthase. Upon deletion of both genes the αGG concentration in culture supernatants was increased from 0.5 mM in C. glutamicum (pEKEx3-ggpSP) to 2.9 mM in C. glutamicum ΔotsA IMglgA (pEKEx3-ggpSP). Upon nitrogen limitation, which inhibits synthesis of amino acids as compatible solutes, C. glutamicum ΔotsA IMglgA (pEKEx3-ggpSP) produced more than 10 mM αGG (about 2 g L−1). Conclusions Corynebacterium glutamicum can be engineered as efficient platform for the production of the compatible solute αGG. Redirection of carbon flux towards αGG synthesis by elimination of the competing pathways for glycogen and trehalose synthesis as well as optimization of nitrogen supply is an efficient strategy to further optimize production of αGG. Electronic supplementary material The online version of this article (10.1186/s12934-018-0939-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin Roenneke
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany.,Gutachterbüro U. Borchardt, Hennef (Sieg), Germany
| | - Natalie Rosenfeldt
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Sami M Derya
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Jens F Novak
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Kay Marin
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany.,Evonik Degussa GmbH, Halle (Westphalia), Germany
| | - Reinhard Krämer
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Gerd M Seibold
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany. .,Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein Allee 11, 89081, Ulm, Germany.
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