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Wu F, Xie X, Du T, Jiang X, Miao W, Wang T. Lactococcus lactis, a bacterium with probiotic functions and pathogenicity. World J Microbiol Biotechnol 2023; 39:325. [PMID: 37776350 DOI: 10.1007/s11274-023-03771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Lactococcus lactis (L. lactis) is the primary organism for lactic acid bacteria (LAB) and is a globally recognized safe microorganism for the regulation of the intestinal micro-ecological balance of animals and improving the immune performance of the host. L. lactis is known to play a commercially important role in feed fortification, milk fermentation, and vaccine production, but pathogenic L. lactis has been isolated from many clinical cases in recent years, such as the brain of silver carp with Lactococcosis, the liver and spleen of diseased waterfowl, milk samples and padding materials with cow mastitis, and blood and urine from human patients with endocarditis. In dairy farming, where L. lactis has been used as a probiotic in the past, however, some studies have found that L. lactis can cause mastitis in cows, but the lack of understanding of the pathogenesis of mastitis in cows caused by L. lactis has become a new problem. The main objective of this review is to analyze the increasingly serious clinical mastitis caused by L. lactis and combined with the wide application of L. lactis as probiotics, to comprehensively discuss the characteristics and diversity of L. lactis.
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Affiliation(s)
- Fan Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinmei Xie
- Elanco (Shanghai)Animal Health Co, Ltd, No.1, Field Middle Road, Wusi Farm, Fengxian District, Shanghai, China
| | - Tao Du
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaodan Jiang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wei Miao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tiancheng Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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Ma J, Long S, Wang J, Gao J, Piao X. Microencapsulated essential oils combined with organic acids improves immune antioxidant capacity and intestinal barrier function as well as modulates the hindgut microbial community in piglets. J Anim Sci Biotechnol 2022; 13:16. [PMID: 35144681 PMCID: PMC8832826 DOI: 10.1186/s40104-021-00670-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Background The objective of this experiment was to evaluate the effect of a combination of microencapsulated essential oils and organic acids (MOA) on growth performance, immuno-antioxidant status, intestinal barrier function and microbial structure of the hindgut in piglets. A total of 120 piglets (Duroc × [Landrace × Yorkshire]; weighted 7.66 ± 1.79 kg, weaned at d 28) were randomly selected and allocated to 3 treatments with 4 replicates per group and 10 piglets per replicate according to the initial body weight and gender. The dietary treatments were as follows: 1) basal diet (Ctrl); 2) Ctrl + chlortetracycline (75 mg/kg) (AGP); 3) Ctrl+ MOA (1500 mg/kg). The experiment period was lasted for 21 d. Results Compared to the Ctrl group, dietary supplemented MOA alleviated (P < 0.05) the diarrhea rate from d 12 to 21, enhanced (P < 0.05) the concentration of serum interlukin-10 and glutathione peroxidase in piglets on d 11 after weaning and serum superoxide dismutase in 21-day piglets. The MOA group also improved (P < 0.05) the apparent digestibility of dry matter (DM), organic matter (OM) and gross energy (GE), up-regulated (P < 0.05) the mRNA expression level of occludin, claudin-1 and mucin-2 in ileum and increased (P < 0.05) the contents of propionic and butyric acids in the cecum of piglets. The MOA group modulated the cecal and colonic microbial community structure and increased (P < 0.05) the abundance of Faecalibacterium and Muribaculaceae in cecum and Streptococcus and Weissella in colon. Additionally, AGP group decreased (P < 0.05) apparent digestibility of DM, OM and GE as well as down-regulated (P < 0.05) relative gene expression level of claudin-1 in duodenum and jejunum, ZO-1 and mucin-1 in jejunum of piglets. Conclusion In summary, dietary supplemented MOA alleviated diarrhea and improved nutrient apparent digestibility in piglets via enhancing immuno-antioxidant properties, increasing digestive enzyme activity, up-regulating the expression of intestinal barrier-related genes, and modifying the microbial community structure of the cecum and colon. Therefore, dietary supplementation with MOA as an alternative to antibiotics was feasible to improve intestinal health of piglets in practical production.
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Affiliation(s)
- Jiayu Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shenfei Long
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jie Gao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangshu Piao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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3
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Kleerebezem M, Bachmann H, van Pelt-KleinJan E, Douwenga S, Smid EJ, Teusink B, van Mastrigt O. Lifestyle, metabolism and environmental adaptation in Lactococcus lactis. FEMS Microbiol Rev 2021; 44:804-820. [PMID: 32990728 DOI: 10.1093/femsre/fuaa033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.
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Affiliation(s)
- Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands
| | - Eunice van Pelt-KleinJan
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Sieze Douwenga
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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Significant Differences in Intestinal Microbial Communities in Aquatic Animals from an Aquaculture Area. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9020104] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
While much attention has been given to the role of animal intestinal microbes, few studies have focused on microbial communities and associated functions in cultured aquatic animals. In this study, high–throughput sequencing was used to analyze intestinal microbial communities and functions in fish, shrimp, crab and razor clams. Alpha diversity analyses showed significant differences in intestinal microbial diversity amongst these aquatic animals, and that shrimp intestines harbored the highest diversity and species numbers. T–test analyses (p < 0.05) showed significant differences in dominant microbial operational taxonomic units (OTUs) between all aquatic animals. Predominant intestinal bacteria included; Gammaproteobacteria, Fusobacteria, Mollicutes, Spirochaetia, Cyanobacteria, Bacteroidia and Bacilli. Similarly, anaerobic bacteria were highly diverse in animal intestines and included; Vibrio, Photobacterium, Cetobacterium, Propionigenium, Candidatus Hepatoplasma, Paraclostridium, and Lactobacillus. Principal co–ordinate analysis indicated that the distribution characteristics of intestinal microbes varied with animal species; in particular, we observed a high variability among shrimp intestinal samples. This variability indicated these genera had suitability for the different intestinal environment. Function prediction analysis indicated significant differences amongst different animals in the major functional groups, and that microbial functional profiles were strongly shaped by the intestinal environment. Thus, this study provides an important reference for future studies investigating crosstalk between aquatic animal hosts and their intestinal microbiota.
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Metras BN, Holle MJ, Parker VJ, Miller MJ, Swanson KS. Assessment of commercial companion animal kefir products for label accuracy of microbial composition and quantity. J Anim Sci 2020; 98:5904066. [PMID: 32914845 DOI: 10.1093/jas/skaa301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Kefir is a fermented beverage containing yeast and bacteria produced by the fermentation of water or milk with kefir grains. Lack of regulation for probiotic-containing fermented food sold for companion dogs and cats creates the potential for misreporting on viable microbial counts, taxonomy, and label claims. In this study, the microbiota of six companion animal kefir products were measured quantitatively using standard plating techniques. Microbial composition of these products was also characterized by using high-resolution, long-read amplicon sequencing of the 16S rRNA gene. Five products (83%) listed specific microorganisms, and four products (66%) guaranteed colony forming units (CFU)/g on their label. To enumerate viable lactic acid bacteria (LAB), two lots of each homogenized product were plated upon opening and following 14 d on deMan Rogosa and Sharpe (MRS) agar and incubated under anaerobic and aerobic conditions. Results from point of opening revealed that all commercial kefir products with a guaranteed CFU/g overstated the number of microorganisms present by at least 1 log, with only one product exceeding 1 × 109 CFU/g. Sequencing results demonstrated that none of the labels claiming specific bacterial genera and species on their labels were correct, and all products contained at least three additional bacterial species above the minimum detectable threshold (0.001% relative abundance) that were not disclosed by the manufacturer. In addition to the incorrect viable CFU and bacterial taxonomies, several of the product labels and websites contained a wide range of health claims, none of which are supported by the companion animal literature. Our results demonstrate a low level of accuracy in the labeling of commercial kefir products intended for use in dogs and cats. Regulatory agencies, veterinarians, pet food professionals, and pet owners must scrutinize these products and demand a higher level of accuracy and quality in the future.
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Affiliation(s)
- Breanna N Metras
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Maxwell J Holle
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Valerie J Parker
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH
| | - Michael J Miller
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Kelly S Swanson
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL
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6
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The large plasmidome of Lactococcus lactis subsp. lactis bv. diacetylactis S50 confers its biotechnological properties. Int J Food Microbiol 2020; 337:108935. [PMID: 33152568 DOI: 10.1016/j.ijfoodmicro.2020.108935] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 01/17/2023]
Abstract
Plasmids are autonomous episomally replicating genetic elements, which carry backbone genes important for the replication and maintenance within their host, and accessory genes that might confer an advantage to their host under specific selective pressure in its ecological niche. The genome of dairy isolate L. lactis subsp. lactis bv. diacetylactis S50 was sequenced using the PacBio SMRT Cell Seq-RSII platform and revealed to possess one of the largest plasmidomes among L. lactis strains studied so far, harboring six plasmids: pS6 (5553 bp), pS7a (7308 bp), pS7b (7266 bp), pS19 (19,027 bp), pS74 (74,256 bp) and pS127 (127,002 bp) in total representing 8.9% of genome size (240,412 bp). Based on predicted plasmid replication proteins and origins it appears that all six plasmids replicate via the theta-type mechanism. The two the largest plasmids (pS74 and pS127), carry a number of genes known to be important for growth and survival in the dairy environment. These genes encode technological functions such as bacteriocin production, protein degradation, magnesium and cobalt/nickel transporters, selenium binding, exopolysaccharides (EPS) production, bacteriophage and stress resistance. Beside genes for replication, the small plasmids (pS6, pS7a, pS7a, and pS19) also carry genes important for mobilization and host survival such as type I restriction-modification (R-M) system, metal transporters, enzymes and transcriptional regulators. All plasmids in S50 strain are mobilizable, containing an oriT sequences, while pS127 is self-conjugative and allows for mobilization of the other plasmids. Small plasmids are prone to structural and segregational instability, while pS127 appeared to be segregationally stable thanks to the possession of two partition systems. The main characteristic of plasmid pS74 is EPS production, while plasmid pS127 is characterized by proteinase and multiple bacteriocins, tra locus, phage abortive systems and metal transporters. In addition to LcnA and LcnB, plasmid pS127 encodes several bacteriocin-pheromone molecules and a new bacteriocin named LcnS50, with narrow spectrum of action limited to lactococci, that has been successfully cloned and heterologously expressed.
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7
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Wei H, Wang H, Tang L, Mu C, Ye C, Chen L, Wang C. High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China. BMC Genomics 2019; 20:829. [PMID: 31703624 PMCID: PMC6842235 DOI: 10.1186/s12864-019-6219-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 10/23/2019] [Indexed: 11/22/2022] Open
Abstract
Background Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. Results Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). Conclusions This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.
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Affiliation(s)
- Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chunyu Ye
- Agricultural and Rural Bureau, Sanmen County, Zhejiang Province, China
| | - Lizhi Chen
- Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
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8
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Iskandar CF, Cailliez-Grimal C, Borges F, Revol-Junelles AM. Review of lactose and galactose metabolism in Lactic Acid Bacteria dedicated to expert genomic annotation. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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Andersen JM, Pedersen CM, Bang-Berthelsen CH. Omics-based comparative analysis of putative mobile genetic elements in Lactococcus lactis. FEMS Microbiol Lett 2019; 366:5487889. [PMID: 31074793 DOI: 10.1093/femsle/fnz102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/09/2019] [Indexed: 12/29/2022] Open
Abstract
Lactococcus lactis is globally used in food fermentation. Genomics is useful to investigate speciation and differential occurrence of (un)desired gene functions, often related to mobile DNA. This study investigates L. lactis for putative chromosomal mobile genetic elements through comparative genomics, and analyses how they contribute to chromosomal variation at strain level. Our work identified 95 loci that may range over 10% of the chromosome size when including prophages, and the loci display a marked differential occurrence in the analysed strains. Analysis of differential transcriptomics data revealed how mobile genetic elements may impact the host physiology in response to conditional changes. This insight in the genetic variation of mobile genetic elements in L. lactis holds potential to further identify important functions related to food and biotechnology applications within this important species.
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Affiliation(s)
- Joakim Mark Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Christine Møller Pedersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
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10
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Kelleher P, Mahony J, Bottacini F, Lugli GA, Ventura M, van Sinderen D. The Lactococcus lactis Pan-Plasmidome. Front Microbiol 2019; 10:707. [PMID: 31019500 PMCID: PMC6458302 DOI: 10.3389/fmicb.2019.00707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 01/01/2023] Open
Abstract
Plasmids are autonomous, self-replicating, extrachromosomal genetic elements that are typically not essential for growth of their host. They may encode metabolic capabilities, which promote the maintenance of these genetic elements, and may allow adaption to specific ecological niches and consequently enhance survival. Genome sequencing of 16 Lactococcus lactis strains revealed the presence of 83 plasmids, including two megaplasmids. The limitations of Pacific Biosciences SMRT sequencing in detecting the total plasmid complement of lactococcal strains is examined, while a combined Illumina/SMRT sequencing approach is proposed to combat these issues. Comparative genome analysis of these plasmid sequences combined with other publicly available plasmid sequence data allowed the definition of the lactococcal plasmidome, and facilitated an investigation into (bio) technologically important plasmid-encoded traits such as conjugation, bacteriocin production, exopolysaccharide (EPS) production, and (bacterio) phage resistance.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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11
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Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. INFECTION GENETICS AND EVOLUTION 2018; 66:130-151. [DOI: 10.1016/j.meegid.2018.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/12/2018] [Accepted: 09/19/2018] [Indexed: 11/21/2022]
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12
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Giaretta S, Treu L, Vendramin V, da Silva Duarte V, Tarrah A, Campanaro S, Corich V, Giacomini A. Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose. Front Microbiol 2018; 9:1765. [PMID: 30131781 PMCID: PMC6090898 DOI: 10.3389/fmicb.2018.01765] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/16/2018] [Indexed: 12/03/2022] Open
Abstract
Streptococcus thermophilus is a species widely used in the dairy industry for its capability to rapidly ferment lactose and lower the pH. The capability to use galactose produced from lactose hydrolysis is strain dependent and most of commercial S. thermophilus strains are galactose-negative (Gal−), although galactose-positive (Gal+) would be more technologically advantageous because this feature could provide additional metabolic products and prevent galactose accumulation in foods. In this study, a next generation sequencing transcriptome approach was used to compare for the first time a Gal+ and a Gal− strain to characterize their whole metabolism and shed light on their different properties, metabolic performance and gene regulation. Transcriptome analysis revealed that all genes of the gal operon were expressed very differently in Gal+ and in the Gal− strains. The expression of several genes involved in mixed acid fermentation, PTS sugars transporter and stress response were found enhanced in Gal+. Conversely, genes related to amino acids, proteins metabolism and CRISPR associated proteins were under-expressed. In addition, the strains showed a diverse series of predicted genes controlled by the transcriptional factor catabolite control protein A (CcpA). Overall, transcriptomic analysis suggests that the Gal+ strain underwent a metabolic remodeling to cope with the changed environmental conditions.
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Affiliation(s)
- Sabrina Giaretta
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | - Laura Treu
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy.,Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veronica Vendramin
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | | | - Armin Tarrah
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | | | - Viviana Corich
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
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13
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Kok J, van Gijtenbeek LA, de Jong A, van der Meulen SB, Solopova A, Kuipers OP. The Evolution of gene regulation research in Lactococcus lactis. FEMS Microbiol Rev 2018; 41:S220-S243. [PMID: 28830093 DOI: 10.1093/femsre/fux028] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/15/2017] [Indexed: 11/12/2022] Open
Abstract
Lactococcus lactis is a major microbe. This lactic acid bacterium (LAB) is used worldwide in the production of safe, healthy, tasteful and nutritious milk fermentation products. Its huge industrial importance has led to an explosion of research on the organism, particularly since the early 1970s. The upsurge in the research on L. lactis coincided not accidentally with the advent of recombinant DNA technology in these years. The development of methods to take out and re-introduce DNA in L. lactis, to clone genes and to mutate the chromosome in a targeted way, to control (over)expression of proteins and, ultimately, the availability of the nucleotide sequence of its genome and the use of that information in transcriptomics and proteomics research have enabled to peek deep into the functioning of the organism. Among many other things, this has provided an unprecedented view of the major gene regulatory pathways involved in nitrogen and carbon metabolism and their overlap, and has led to the blossoming of the field of L. lactis systems biology. All of these advances have made L. lactis the paradigm of the LAB. This review will deal with the exciting path along which the research on the genetics of and gene regulation in L. lactis has trodden.
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Affiliation(s)
- Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Lieke A van Gijtenbeek
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Sjoerd B van der Meulen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ana Solopova
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
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14
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Engholm DH, Kilian M, Goodsell DS, Andersen ES, Kjærgaard RS. A visual review of the human pathogen Streptococcus pneumoniae. FEMS Microbiol Rev 2018; 41:854-879. [PMID: 29029129 DOI: 10.1093/femsre/fux037] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Abstract
Being the principal causative agent of bacterial pneumonia, otitis media, meningitis and septicemia, the bacterium Streptococcus pneumoniae is a major global health problem. To highlight the molecular basis of this problem, we have portrayed essential biological processes of the pneumococcal life cycle in eight watercolor paintings. The paintings are done to a consistent nanometer scale based on currently available data from structural biology and proteomics. In this review article, the paintings are used to provide a visual review of protein synthesis, carbohydrate metabolism, cell wall synthesis, cell division, teichoic acid synthesis, virulence, transformation and pilus synthesis based on the available scientific literature within the field of pneumococcal biology. Visualization of the molecular details of these processes reveals several scientific questions about how molecular components of the pneumococcal cell are organized to allow biological function to take place. By the presentation of this visual review, we intend to stimulate scientific discussion, aid in the generation of scientific hypotheses and increase public awareness. A narrated video describing the biological processes in the context of a whole-cell illustration accompany this article.
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Affiliation(s)
- Ditte Høyer Engholm
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Rutgers, the State University of New Jersey, NJ 08901, USA
| | - Ebbe Sloth Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark
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15
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The late blowing defect of hard cheeses: Behaviour of cells and spores of Clostridium tyrobutyricum throughout the cheese manufacturing and ripening. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.08.083] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Golomb BL, Yu AO, Coates LC, Marco ML. The Lactococcus lactis KF147 nonribosomal peptide synthetase/polyketide synthase system confers resistance to oxidative stress during growth on plant leaf tissue lysate. Microbiologyopen 2017; 7. [PMID: 28921941 PMCID: PMC5822349 DOI: 10.1002/mbo3.531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/07/2023] Open
Abstract
Strains of Lactococcus lactis isolated from plant tissues possess adaptations that support their survival and growth in plant‐associated microbial habitats. We previously demonstrated that genes coding for a hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) system involved in production of an uncharacterized secondary metabolite are specifically induced in L. lactis KF147 during growth on plant tissues. Notably, this NRPS/PKS has only been identified in plant‐isolated strains of L. lactis. Here, we show that the L. lactis KF147 NRPS/PKS genes have homologs in certain Streptococcus mutans isolates and the genetic organization of the NRPS/PKS locus is conserved among L. lactis strains. Using an L. lactis KF147 mutant deficient in synthesis of NrpC, a 4′‐phosphopantetheinyl transferase, we found that the NRPS/PKS system improves L. lactis during growth under oxidative conditions in Arapidopsis thaliana leaf lysate. The NRPS/PKS system also improves tolerance of L. lactis to reactive oxygen species and specifically H2O2 and superoxide radicals in culture medium. These findings indicate that this secondary metabolite provides a novel mechanism for reactive oxygen species detoxification not previously known for this species.
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Affiliation(s)
- Benjamin L Golomb
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Annabelle O Yu
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Laurynne C Coates
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, CA, USA
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17
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Díez L, Solopova A, Fernández-Pérez R, González M, Tenorio C, Kuipers OP, Ruiz-Larrea F. Transcriptome analysis shows activation of the arginine deiminase pathway in Lactococcus lactis as a response to ethanol stress. Int J Food Microbiol 2017. [DOI: 10.1016/j.ijfoodmicro.2017.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Ruiz Rodríguez LG, Aller K, Bru E, De Vuyst L, Hébert EM, Mozzi F. Enhanced mannitol biosynthesis by the fruit origin strain Fructobacillus tropaeoli CRL 2034. Appl Microbiol Biotechnol 2017; 101:6165-6177. [PMID: 28674850 DOI: 10.1007/s00253-017-8395-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/30/2022]
Abstract
Mannitol is a natural low-calorie sugar alcohol produced by certain (micro)organisms applicable in foods for diabetics due to its zero glycemic index. In this work, we evaluated mannitol production and yield by the fruit origin strain Fructobacillus tropaeoli CRL 2034 using response surface methodology with central composite design (CCD) as optimization strategy. The effect of the total saccharide (glucose + fructose, 1:2) content (TSC) in the medium (75, 100, 150, 200, and 225 g/l) and stirring (S; 50, 100, 200, 300 and 350 rpm) on mannitol production and yield by this strain was evaluated by using a 22 full-factorial CCD with 4 axial points (α = 1.5) and four replications of the center point, leading to 12 random experimental runs. Fermentations were carried out at 30 °C and pH 5.0 for 24 h. Minitab-15 software was used for experimental design and data analyses. The multiple response prediction analysis established 165 g/l of TSC and 200 rpm of S as optimal culture conditions to reach 85.03 g/l [95% CI (78.68, 91.39)] of mannitol and a yield of 82.02% [95% CI (71.98, 92.06)]. Finally, a validation experiment was conducted at the predicted optimum levels. The results obtained were 81.91 g/l of mannitol with a yield of 77.47% in outstanding agreement with the expected values. The mannitol 2-dehydrogenase enzyme activity was determined with 4.6-4.9 U/mg as the highest value found. To conclude, F. tropaeoli CRL 2034 produced high amounts of high-quality mannitol from fructose, being an excellent candidate for this polyol production.
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Affiliation(s)
- Luciana G Ruiz Rodríguez
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000, Tucumán, Argentina
| | - Kadri Aller
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000, Tucumán, Argentina.,Center for Food and Fermentation Technologies, Akadeemia tee 15A, 12618, Tallinn, Estonia
| | - Elena Bru
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000, Tucumán, Argentina
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Elvira M Hébert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000, Tucumán, Argentina
| | - Fernanda Mozzi
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, T4000, Tucumán, Argentina.
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19
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Integrated proteomic and metabolomic analysis reveals that rhodomyrtone reduces the capsule in Streptococcus pneumoniae. Sci Rep 2017; 7:2715. [PMID: 28578394 PMCID: PMC5457420 DOI: 10.1038/s41598-017-02996-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/21/2017] [Indexed: 01/12/2023] Open
Abstract
The emergence of antibiotic-resistant pathogenic bacteria is a healthcare problem worldwide. We evaluated the antimicrobial activity of rhodomyrtone, an acylphloroglucinol present in Rhodomyrtus tomentosa leaves, against the human Gram-positive pathogen Streptococcus pneumoniae. The compound exhibited pronounced anti-pneumococcal activity against a broad collection of clinical isolates. We studied the effects at the molecular level by integrated proteomic and metabolomic analysis. The results revealed alterations in enzymes and metabolites involved in several metabolic pathways including amino acid biosynthesis, nucleic acid biosynthesis, glucid, and lipid metabolism. Notably, the levels of two enzymes (glycosyltransferase and UTP-glucose-1-phosphate uridylyltransferase) and three metabolites (UDP-glucose, UDP-glucuronic acid and UDP-N-acetyl-D-galactosamine) participating in the synthesis of the pneumococcal capsule clearly diminished in the bacterial cells exposed to rhodomyrtone. Rhodomyrtone-treated pneumococci significantly possessed less amount of capsule, as measured by a colorimetric assay and visualized by electron microscopy. These findings reveal the utility of combining proteomic and metabolomic analyses to provide insight into phenotypic features of S. pneumoniae treated with this potential novel antibiotic. This can lead to an alternative antibiotic for the treatment of S. pneumoniae infections, because of the growing concern regarding antimicrobial resistance.
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20
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GC-MS based metabolomics analysis reveals the effects of different agitation speeds on the level of proteinogenic amino acids in Lactococcus lactis subsp. cremoris MG1363. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1268-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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21
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Song AAL, In LLA, Lim SHE, Rahim RA. A review on Lactococcus lactis: from food to factory. Microb Cell Fact 2017; 16:55. [PMID: 28376880 PMCID: PMC5379754 DOI: 10.1186/s12934-017-0669-x] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 03/28/2017] [Indexed: 02/08/2023] Open
Abstract
Lactococcus lactis has progressed a long way since its discovery and initial use in dairy product fermentation, to its present biotechnological applications in genetic engineering for the production of various recombinant proteins and metabolites that transcends the heterologous species barrier. Key desirable features of this gram-positive lactic acid non-colonizing gut bacteria include its generally recognized as safe (GRAS) status, probiotic properties, the absence of inclusion bodies and endotoxins, surface display and extracellular secretion technology, and a diverse selection of cloning and inducible expression vectors. This have made L. lactis a desirable and promising host on par with other well established model bacterial or yeast systems such as Escherichia coli, Saccharomyces [corrected] cerevisiae and Bacillus subtilis. In this article, we review recent technological advancements, challenges, future prospects and current diversified examples on the use of L. lactis as a microbial cell factory. Additionally, we will also highlight latest medical-based applications involving whole-cell L. lactis as a live delivery vector for the administration of therapeutics against both communicable and non-communicable diseases.
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Affiliation(s)
- Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology & Biomolecular Sciences, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Lionel L A In
- Functional Food Research Group, Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Swee Hua Erin Lim
- Perdana University-Royal College of Surgeons in Ireland, Perdana University, Block B and D, MAEPS Building, MARDI Complex, Jalan MAEPS Perdana, 43400, Serdang, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell & Molecular Biology, Faculty of Biotechnology & Biomolecular Sciences, University Putra Malaysia, Serdang, Selangor, Malaysia
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22
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Development of a simple, low-cost and eurytopic medium based on Pleurotus eryngii for lactic acid bacteria. AMB Express 2016; 6:65. [PMID: 27590888 PMCID: PMC5010549 DOI: 10.1186/s13568-016-0235-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/18/2016] [Indexed: 11/10/2022] Open
Abstract
Lactic acid bacteria (LAB) are a group of important beneficial microorganisms for human, but their growth is restricted to the habitats with rich nutrients. In order to develop a simple, low-cost and efficient medium based on the mushroom Pleurotus eryngii, this study evaluated the effects of different treatment methods for the mushroom, concentration of the mushroom, buffers, tween 80, MgSO4·7H2O, MnSO4·4H2O, CuSO4·5H2O, riboflavin and ascorbic acid on the growth of Lactococcus lactis subsp. lactis SLPE1-3. An optimized medium was developed, which was composed of the mushroom at 200 g/L, the buffer sodium acetate at 5 g/L, and riboflavin at 0.5 mg/L. The mushroom was ground, boiled and filtered for the filtrate in advance. In this optimized medium which was named as PSR medium, the population density of SLPE1-3 sharply reached 2.13 × 10(9) CFU/mL within 18 h of incubation, and still maintained 1.17 × 10(8) CFU/mL at 120 h. In addition, this study found that 6 kinds of LAB could grow almost well, and maintained high survival in PSR medium compared to M17 or MRS medium, including Lactococcus lactis subsp. lactis, Lactobacillus plantarum, Lactococcus lactis subsp. cremoris, Lactobacillus paracasei, Pediococcus pentosaceus and Lactobacillus rhamnosus. These results showed that PSR medium was a simple, low cost and eurytopic medium for the cultivation of LAB, and could replace MRS or M17 medium in the food industry, biomedicine and laboratory.
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23
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Genes associated to lactose metabolism illustrate the high diversity of Carnobacterium maltaromaticum. Food Microbiol 2016; 58:79-86. [PMID: 27217362 DOI: 10.1016/j.fm.2016.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 11/20/2022]
Abstract
The dairy population of Carnobacterium maltaromaticum is characterized by a high diversity suggesting a high diversity of the genetic traits linked to the dairy process. As lactose is the main carbon source in milk, the genetics of lactose metabolism was investigated in this LAB. Comparative genomic analysis revealed that the species C. maltaromaticum exhibits genes related to the Leloir and the tagatose-6-phosphate (Tagatose-6P) pathways. More precisely, strains can bear genes related to one or both pathways and several strains apparently do not contain homologs related to these pathways. Analysis at the population scale revealed that the Tagatose-6P and the Leloir encoding genes are disseminated in multiple phylogenetic lineages of C. maltaromaticum: genes of the Tagatose-6P pathway are present in the lineages I, II and III, and genes of the Leloir pathway are present in the lineages I, III and IV. These data suggest that these genes evolved thanks to horizontal transfer, genetic duplication and translocation. We hypothesize that the lac and gal genes evolved in C. maltaromaticum according to a complex scenario that mirrors the high population diversity.
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24
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Mistou MY, Sutcliffe IC, van Sorge NM. Bacterial glycobiology: rhamnose-containing cell wall polysaccharides in Gram-positive bacteria. FEMS Microbiol Rev 2016; 40:464-79. [PMID: 26975195 PMCID: PMC4931226 DOI: 10.1093/femsre/fuw006] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
The composition of the Gram-positive cell wall is typically described as containing peptidoglycan, proteins and essential secondary cell wall structures called teichoic acids, which comprise approximately half of the cell wall mass. The cell walls of many species within the genera Streptococcus, Enterococcus and Lactococcus contain large amounts of the sugar rhamnose, which is incorporated in cell wall-anchored polysaccharides (CWP) that possibly function as homologues of well-studied wall teichoic acids (WTA). The presence and chemical structure of many rhamnose-containing cell wall polysaccharides (RhaCWP) has sometimes been known for decades. In contrast to WTA, insight into the biosynthesis and functional role of RhaCWP has been lacking. Recent studies in human streptococcal and enterococcal pathogens have highlighted critical roles for these complex polysaccharides in bacterial cell wall architecture and pathogenesis. In this review, we provide an overview of the RhaCWP with regards to their biosynthesis, genetics and biological function in species most relevant to human health. We also briefly discuss how increased knowledge in this field can provide interesting leads for new therapeutic compounds and improve biotechnological applications. This review summarizes new insights into the genetics and function of rhamnose-containing cell wall polysaccharides expressed by lactic acid bacteria, which includes medically important pathogens, and discusses perspectives on possible future therapeutic and biotechnological applications.
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Affiliation(s)
- Michel-Yves Mistou
- Laboratory for Food Safety, Université Paris-Est, ANSES, F-94701 Maisons-Alfort, France
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Nina M van Sorge
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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25
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Wang W, Cao J, Yang F, Wang X, Zheng S, Sharshov K, Li L. High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet. Microbiologyopen 2016; 5:287-95. [PMID: 26842811 PMCID: PMC4831473 DOI: 10.1002/mbo3.327] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 12/16/2022] Open
Abstract
Elucidating the spatial dynamic and core gut microbiome related to wild bar‐headed goose is of crucial importance for probiotics development that may meet the demands of bar‐headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar‐headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar‐headed geese gut microbial communities by Illumina high‐throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar‐headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in‐depth assessment, to date, of the gut microbes that associated with bar‐headed geese. These data create a baseline for future bar‐headed goose microbiology research, and make an original contribution to probiotics development for bar‐headed goose artificial breeding industries.
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Affiliation(s)
- Wen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China.,Center of Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, 610000, China
| | - Jian Cao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China.,University of the Chinese Academy of Sciences, Beijing, 100101,, China
| | - Fang Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China
| | - Xuelian Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China
| | - Sisi Zheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China.,University of the Chinese Academy of Sciences, Beijing, 100101,, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, 630117, Russia
| | - Laixing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China
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26
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Lysozyme affects the microbial catabolism of free arginine in raw-milk hard cheeses. Food Microbiol 2016; 57:16-22. [PMID: 27052697 DOI: 10.1016/j.fm.2015.11.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 11/22/2022]
Abstract
Lysozyme (LZ) is used in several cheese varieties to prevent late blowing which results from fermentation of lactate by Clostridium tyrobutyricum. Side effects of LZ on lactic acid bacteria population and free amino acid pattern were studied in 16 raw-milk hard cheeses produced in eight parallel cheese makings conducted at four different dairies using the same milk with (LZ+) or without (LZ-) addition of LZ. The LZ-cheeses were characterized by higher numbers of cultivable microbial population and lower amount of DNA arising from lysed bacterial cells with respect to LZ + cheeses. At both 9 and 16 months of ripening, Lactobacillus delbrueckii and Lactobacillus fermentum proved to be the species mostly affected by LZ. The total content of free amino acids indicated the proteolysis extent to be characteristic of the dairy, regardless to the presence of LZ. In contrast, the relative patterns showed the microbial degradation of arginine to be promoted in LZ + cheeses. The data demonstrated that the arginine-deiminase pathway was only partially adopted since citrulline represented the main product and only trace levels of ornithine were found. Differences in arginine degradation were considered for starter and non-starter lactic acid bacteria, at different cheese ripening stages.
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27
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Yeung TW, Arroyo-Maya IJ, McClements DJ, Sela DA. Microencapsulation of probiotics in hydrogel particles: enhancing Lactococcus lactis subsp. cremoris LM0230 viability using calcium alginate beads. Food Funct 2016; 7:1797-804. [DOI: 10.1039/c5fo00801h] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Encapsulation in alginate improved the viability of lactococcal probiotics.
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Affiliation(s)
| | | | - David J. McClements
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
- Department of Biochemistry
| | - David A. Sela
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
- Center for Bioactive Delivery
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28
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Krumbeck JA, Marsteller NL, Frese SA, Peterson DA, Ramer-Tait AE, Hutkins RW, Walter J. Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract. Environ Microbiol 2015; 18:2172-84. [PMID: 26530032 DOI: 10.1111/1462-2920.13108] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/27/2015] [Indexed: 02/06/2023]
Abstract
Rodent-derived strains of Lactobacillus reuteri densely colonize the forestomach of mice and possess several genes whose predicted functions constitute adaptations towards an acidic environment. The objective of this study was to systematically determine which genes of L. reuteri 100-23 contribute to tolerance towards host gastric acid secretion. Genes predicted to be involved in acid resistance were inactivated, and their contribution to survival under acidic conditions was confirmed in model gastric juice. Fitness of five mutants that showed impaired in vitro acid resistance were then compared through competition experiments in ex-germ-free mice that were either treated with omeprazole, a proton-pump inhibitor that suppresses acid secretion in the stomach, or left untreated. This analysis revealed that the urease cluster was the predominant factor in mediating resistance to gastric acid production. Population levels of the mutant, which were substantially decreased in untreated mice, were almost completely restored through omeprazole, demonstrating that urease production in L. reuteri is mainly devoted to overcome gastric acid. The findings provide novel information on the mechanisms by which L. reuteri colonizes its gastric niche and demonstrate that in silico gene predictions and in vitro tests have limitations for predicting the ecological functions of colonization factors in bacterial symbionts.
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Affiliation(s)
- Janina A Krumbeck
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.,School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Nathan L Marsteller
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Steven A Frese
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Daniel A Peterson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Robert W Hutkins
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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29
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Tikhomirova A, Trappetti C, Paton JC, Kidd SP. The outcome of H. influenzae and S. pneumoniae inter-species interactions depends on pH, nutrient availability and growth phase. Int J Med Microbiol 2015; 305:881-92. [PMID: 26481153 DOI: 10.1016/j.ijmm.2015.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/07/2015] [Accepted: 09/10/2015] [Indexed: 01/16/2023] Open
Abstract
Haemophilus influenzae and Streptococcus pneumoniae exist together as common commensals of the healthy human nasopharynx, but both are important aetiological agents of different diseases, including the paediatric disease otitis media. It was recently shown that the formation of a multispecies biofilm of H. influenzae and S. pneumoniae is the cause of chronic forms of otitis media. However, the interactions between the two species are not clearly defined. Using a defined and kinetic analysis, our study has shown that while co-existence of the two species occurs, S. pneumoniae is also able to convert H. influenzae to a non-culturable state. We determined that this process was dependent on growth phase and pH. To analyse the H. influenzae/S. pneumoniae interactions in more depth, we investigated the growth and transcriptional profile in a pH-defined batch culture model, as well as in a growth phase independent flow cell system. Transcriptomics has shown that there are changes in gene expression in each of the species when grown in co-culture, intriguingly inducing the S. pneumoniae bacteriocin transport genes, and phage-associated genes in both species. Importantly, we have shown vast changes in gene expression in a group of S. pneumoniae metabolic genes, including those encoding lactose utilisation, glycerol utilisation and sugar transport proteins; we have shown that the expression of these genes depends not only on the presence of H. influenzae, but also on the growth system utilised.
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Affiliation(s)
- Alexandra Tikhomirova
- Research Centre for Infectious Disease, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Claudia Trappetti
- Research Centre for Infectious Disease, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - James C Paton
- Research Centre for Infectious Disease, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Stephen P Kidd
- Research Centre for Infectious Disease, School of Biological Sciences, The University of Adelaide, Adelaide, Australia.
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30
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Gibbons JG, Rinker DC. The genomics of microbial domestication in the fermented food environment. Curr Opin Genet Dev 2015; 35:1-8. [PMID: 26338497 DOI: 10.1016/j.gde.2015.07.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/10/2015] [Accepted: 07/16/2015] [Indexed: 02/07/2023]
Abstract
Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.
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Affiliation(s)
- John G Gibbons
- Biology Department, Clark University, 950 Main Street, Worcester, MA, USA.
| | - David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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31
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Papadimitriou K, Pot B, Tsakalidou E. How microbes adapt to a diversity of food niches. Curr Opin Food Sci 2015. [DOI: 10.1016/j.cofs.2015.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Aller K, Adamberg K, Reile I, Timarova V, Peebo K, Vilu R. Excess of threonine compared with serine promotes threonine aldolase activity in Lactococcus lactis IL1403. MICROBIOLOGY-SGM 2015; 161:1073-1080. [PMID: 25743155 DOI: 10.1099/mic.0.000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/03/2015] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis is an important lactic acid starter for food production as well as a cell factory for production of food grade additives, among which natural flavour production is one of the main interests of food producers. Flavour production is associated with the degradation of amino acids and comprehensive studies are required to elucidate mechanisms behind these pathways. In this study using chemically defined medium, labelled substrate and steady-state cultivation, new data for the catabolism of threonine in Lc. lactis have been obtained. The biosynthesis of glycine in this organism is associated with the catabolic pathways of glucose and serine. Nevertheless, if threonine concentration in the growth environment exceeds that of serine, threonine becomes the main source for glycine biosynthesis and the utilization of serine decreases. Also, the conversion of threonine to glycine was initiated by a threonine aldolase and this was the principal pathway used for threonine degradation. As in Streptococcus thermophilus, serine hydroxymethyltransferase in Lc. lactis may possess a secondary activity as threonine aldolase. Other catabolic pathways of threonine (e.g. threonine dehydrogenase and threonine dehydratase) were not detected.
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Affiliation(s)
- Kadri Aller
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Kaarel Adamberg
- Tallinn University of Technology, Department of Food Processing, Ehitajate tee 5, Tallinn 19086, Estonia.,Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Indrek Reile
- National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Veronica Timarova
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Karl Peebo
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
| | - Raivo Vilu
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, Tallinn 12618, Estonia.,Competence Center of Food and Fermentation Technologies, Akadeemia tee 15A, Tallinn 12618, Estonia
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33
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Richards VP, Palmer SR, Pavinski Bitar PD, Qin X, Weinstock GM, Highlander SK, Town CD, Burne RA, Stanhope MJ. Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol 2015; 6:741-53. [PMID: 24625962 PMCID: PMC4007547 DOI: 10.1093/gbe/evu048] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.
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Affiliation(s)
- Vincent P Richards
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
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Cavanagh D, Fitzgerald GF, McAuliffe O. From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment. Food Microbiol 2014; 47:45-61. [PMID: 25583337 DOI: 10.1016/j.fm.2014.11.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/22/2014] [Accepted: 11/01/2014] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.
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Affiliation(s)
- Daniel Cavanagh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Microbiology, University College Cork, Co. Cork, Ireland.
| | | | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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35
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Lactococcus lactis metabolism and gene expression during growth on plant tissues. J Bacteriol 2014; 197:371-81. [PMID: 25384484 DOI: 10.1128/jb.02193-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria have been isolated from living, harvested, and fermented plant materials; however, the adaptations these bacteria possess for growth on plant tissues are largely unknown. In this study, we investigated plant habitat-specific traits of Lactococcus lactis during growth in an Arabidopsis thaliana leaf tissue lysate (ATL). L. lactis KF147, a strain originally isolated from plants, exhibited a higher growth rate and reached 7.9-fold-greater cell densities during growth in ATL than the dairy-associated strain L. lactis IL1403. Transcriptome profiling (RNA-seq) of KF147 identified 853 induced and 264 repressed genes during growth in ATL compared to that in GM17 laboratory culture medium. Genes induced in ATL included those involved in the arginine deiminase pathway and a total of 140 carbohydrate transport and metabolism genes, many of which are involved in xylose, arabinose, cellobiose, and hemicellulose metabolism. The induction of those genes corresponded with L. lactis KF147 nutrient consumption and production of metabolic end products in ATL as measured by gas chromatography-time of flight mass spectrometry (GC-TOF/MS) untargeted metabolomic profiling. To assess the importance of specific plant-inducible genes for L. lactis growth in ATL, xylose metabolism was targeted for gene knockout mutagenesis. Wild-type L. lactis strain KF147 but not an xylA deletion mutant was able to grow using xylose as the sole carbon source. However, both strains grew to similarly high levels in ATL, indicating redundancy in L. lactis carbohydrate metabolism on plant tissues. These findings show that certain strains of L. lactis are well adapted for growth on plants and possess specific traits relevant for plant-based food, fuel, and feed fermentations.
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36
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Lactate dehydrogenase is the key enzyme for pneumococcal pyruvate metabolism and pneumococcal survival in blood. Infect Immun 2014; 82:5099-109. [PMID: 25245810 DOI: 10.1128/iai.02005-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae is a fermentative microorganism and causes serious diseases in humans, including otitis media, bacteremia, meningitis, and pneumonia. However, the mechanisms enabling pneumococcal survival in the host and causing disease in different tissues are incompletely understood. The available evidence indicates a strong link between the central metabolism and pneumococcal virulence. To further our knowledge on pneumococcal virulence, we investigated the role of lactate dehydrogenase (LDH), which converts pyruvate to lactate and is an essential enzyme for redox balance, in the pneumococcal central metabolism and virulence using an isogenic ldh mutant. Loss of LDH led to a dramatic reduction of the growth rate, pinpointing the key role of this enzyme in fermentative metabolism. The pattern of end products was altered, and lactate production was totally blocked. The fermentation profile was confirmed by in vivo nuclear magnetic resonance (NMR) measurements of glucose metabolism in nongrowing cell suspensions of the ldh mutant. In this strain, a bottleneck in the fermentative steps is evident from the accumulation of pyruvate, revealing LDH as the most efficient enzyme in pyruvate conversion. An increase in ethanol production was also observed, indicating that in the absence of LDH the redox balance is maintained through alcohol dehydrogenase activity. We also found that the absence of LDH renders the pneumococci avirulent after intravenous infection and leads to a significant reduction in virulence in a model of pneumonia that develops after intranasal infection, likely due to a decrease in energy generation and virulence gene expression.
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Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D. The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 2014; 38:1066-88. [PMID: 24861818 DOI: 10.1111/1574-6976.12074] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 01/20/2023] Open
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
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Affiliation(s)
- Stuart Ainsworth
- Department of Microbiology, University College Cork, Cork, Ireland
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38
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Aller K, Adamberg K, Timarova V, Seiman A, Feštšenko D, Vilu R. Nutritional requirements and media development for Lactococcus lactis IL1403. Appl Microbiol Biotechnol 2014; 98:5871-81. [PMID: 24626960 DOI: 10.1007/s00253-014-5641-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/21/2014] [Accepted: 02/28/2014] [Indexed: 11/29/2022]
Abstract
Lactic acid bacteria are extensively used in food technology and for the production of various compounds, but they are fastidious in nutrient requirements. In order to elucidate the role of each component precisely, defined multicomponent media are required. This study focuses on determining nutrient auxotrophies and minimizing media components (amino acids, vitamins, metal ions, buffers and additional compounds) for the cultivation of Lactococcus lactis subsp. lactis IL1403, using microtitre plates and test tubes. It was shown that glutamine and asparagine were the most important media components for achieving higher biomass yields while the branched-chain amino acids were necessary to increase specific growth rate. The amino acid and glucose ratio was reduced to achieve minimal residual concentration of amino acids in the medium after the growth of cells, whereas the specific growth rate and biomass yield of cells were not considerably affected. As the percentage of each consumed amino acid compared to initial amount is larger than measurement error, these optimized media are important for achieving more precise data about amino acid utilization and metabolism.
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Affiliation(s)
- Kadri Aller
- The Competence Center of Food and Fermentation Technologies (CCFFT), Akadeemia tee 15A, 12618, Tallinn, Estonia,
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39
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Montel MC, Buchin S, Mallet A, Delbes-Paus C, Vuitton DA, Desmasures N, Berthier F. Traditional cheeses: rich and diverse microbiota with associated benefits. Int J Food Microbiol 2014; 177:136-54. [PMID: 24642348 DOI: 10.1016/j.ijfoodmicro.2014.02.019] [Citation(s) in RCA: 354] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 02/17/2014] [Accepted: 02/22/2014] [Indexed: 11/26/2022]
Abstract
The risks and benefits of traditional cheeses, mainly raw milk cheeses, are rarely set out objectively, whence the recurrent confused debate over their pros and cons. This review starts by emphasizing the particularities of the microbiota in traditional cheeses. It then describes the sensory, hygiene, and possible health benefits associated with traditional cheeses. The microbial diversity underlying the benefits of raw milk cheese depends on both the milk microbiota and on traditional practices, including inoculation practices. Traditional know-how from farming to cheese processing helps to maintain both the richness of the microbiota in individual cheeses and the diversity between cheeses throughout processing. All in all more than 400 species of lactic acid bacteria, Gram and catalase-positive bacteria, Gram-negative bacteria, yeasts and moulds have been detected in raw milk. This biodiversity decreases in cheese cores, where a small number of lactic acid bacteria species are numerically dominant, but persists on the cheese surfaces, which harbour numerous species of bacteria, yeasts and moulds. Diversity between cheeses is due particularly to wide variations in the dynamics of the same species in different cheeses. Flavour is more intense and rich in raw milk cheeses than in processed ones. This is mainly because an abundant native microbiota can express in raw milk cheeses, which is not the case in cheeses made from pasteurized or microfiltered milk. Compared to commercial strains, indigenous lactic acid bacteria isolated from milk/cheese, and surface bacteria and yeasts isolated from traditional brines, were associated with more complex volatile profiles and higher scores for some sensorial attributes. The ability of traditional cheeses to combat pathogens is related more to native antipathogenic strains or microbial consortia than to natural non-microbial inhibitor(s) from milk. Quite different native microbiota can protect against Listeria monocytogenes in cheeses (in both core and surface) and on the wooden surfaces of traditional equipment. The inhibition seems to be associated with their qualitative and quantitative composition rather than with their degree of diversity. The inhibitory mechanisms are not well elucidated. Both cross-sectional and cohort studies have evidenced a strong association of raw-milk consumption with protection against allergic/atopic diseases; further studies are needed to determine whether such association extends to traditional raw-milk cheese consumption. In the future, the use of meta-omics methods should help to decipher how traditional cheese ecosystems form and function, opening the way to new methods of risk-benefit management from farm to ripened cheese.
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Affiliation(s)
| | - Solange Buchin
- INRA, UR342 Technologie et Analyses Laitières, F-39801 Poligny, France
| | - Adrien Mallet
- Normandie Univ, France; UNICAEN, ABTE, F-14032 Caen, France
| | - Céline Delbes-Paus
- INRA, Unité Recherches Fromagères, 20 Côte de Reyne, F-15000 Aurillac, France
| | - Dominique A Vuitton
- UNICAEN, ABTE, F-14032 Caen, France; EA3181/Université de Franche-Comté, 25030, Besançon, France
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40
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Global transcriptome analysis of Lactococcus garvieae strains in response to temperature. PLoS One 2013; 8:e79692. [PMID: 24223997 PMCID: PMC3817100 DOI: 10.1371/journal.pone.0079692] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/24/2013] [Indexed: 11/19/2022] Open
Abstract
Lactococcus garvieae is an important fish and an opportunistic human pathogen. The genomic sequences of several L. garvieae strains have been recently published, opening the possibility of global studies on the biology of this pathogen. In this study, a whole genome DNA microarray of two strains of L. garvieae was designed and validated. This DNA microarray was used to investigate the effects of growth temperature (18°C and 37°C) on the transcriptome of two clinical strains of L. garvieae that were isolated from fish (Lg8831) and from a human case of septicemia (Lg21881). The transcriptome profiles evidenced a strain-specific response to temperature, which was more evident at 18°C. Among the most significant findings, Lg8831 was found to up-regulate at 18°C several genes encoding different cold-shock and cold-induced proteins involved in an efficient adaptive response of this strain to low-temperature conditions. Another relevant result was the description, for the first time, of respiratory metabolism in L. garvieae, whose gene expression regulation was temperature-dependent in Lg21881. This study provides new insights about how environmental factors such as temperature can affect L. garvieae gene expression. These data could improve our understanding of the regulatory networks and adaptive biology of this important pathogen.
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41
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Carvalho SM, Farshchi Andisi V, Gradstedt H, Neef J, Kuipers OP, Neves AR, Bijlsma JJE. Pyruvate oxidase influences the sugar utilization pattern and capsule production in Streptococcus pneumoniae. PLoS One 2013; 8:e68277. [PMID: 23844180 PMCID: PMC3701046 DOI: 10.1371/journal.pone.0068277] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 06/02/2013] [Indexed: 11/18/2022] Open
Abstract
Pyruvate oxidase is a key function in the metabolism and lifestyle of many lactic acid bacteria and its activity depends on the presence of environmental oxygen. In Streptococcus pneumoniae the protein has been suggested to play a major role in metabolism and has been implicated in virulence, oxidative stress survival and death in stationary phase. Under semi-aerobic conditions, transcriptomic and metabolite profiling analysis of a spxB mutant grown on glucose showed minor changes compared to the wild type, apart from the significant induction of two operons involved in carbohydrate uptake and processing. This induction leads to a change in the sugar utilization capabilities of the bacterium, as indicated by the analysis of the growth profiles of the D39 parent and spxB mutant on alternative carbohydrates. Metabolic analysis and growth experiments showed that inactivation of SpxB has no effect on the glucose fermentation pattern, except under aerobic conditions. More importantly, we show that mutation of spxB results in the production of increased amounts of capsule, the major virulence factor of S. pneumoniae. Part of this increase can be attributed to induction of capsule operon (cps) transcription. Therefore, we propose that S. pneumoniae utilizes pyruvate oxidase as an indirect sensor of the oxygenation of the environment, resulting in the adaption of its nutritional capability and the amount of capsule to survive in the host.
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Affiliation(s)
- Sandra M. Carvalho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vahid Farshchi Andisi
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Henrik Gradstedt
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolanda Neef
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ana R. Neves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jetta J. E. Bijlsma
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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42
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Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. J Biol Chem 2013; 288:21295-21306. [PMID: 23720742 DOI: 10.1074/jbc.m113.458265] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite high similarity in sequence and catalytic properties, the l-lactate dehydrogenases (LDHs) in lactic acid bacteria (LAB) display differences in their regulation that may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose 1,6-bisphosphate (FBP), phosphate (Pi), and ionic strength (NaCl concentration) on six LDHs from four LABs studied at pH 6 and pH 7. We found that 1) the extent of activation by FBP (Kact) differs. Lactobacillus plantarum LDH is not regulated by FBP, but the other LDHs are activated with increasing sensitivity in the following order: Enterococcus faecalis LDH2 ≤ Lactococcus lactis LDH2 < E. faecalis LDH1 < L. lactis LDH1 ≤ Streptococcus pyogenes LDH. This trend reflects the electrostatic properties in the allosteric binding site of the LDH enzymes. 2) For L. plantarum, S. pyogenes, and E. faecalis, the effects of Pi are distinguishable from the effect of changing ionic strength by adding NaCl. 3) Addition of Pi inhibits E. faecalis LDH2, whereas in the absence of FBP, Pi is an activator of S. pyogenes LDH, E. faecalis LDH1, and L. lactis LDH1 and LDH2 at pH 6. These effects can be interpreted by considering the computed binding affinities of Pi to the catalytic and allosteric binding sites of the enzymes modeled in protonation states corresponding to pH 6 and pH 7. Overall, the results show a subtle interplay among the effects of Pi, FBP, and pH that results in different regulatory effects on the LDHs of different LABs.
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Affiliation(s)
- Anna Feldman-Salit
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,; BioQuant and
| | - Silvio Hering
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Hanan L Messiha
- Manchester Centre for Integrative Systems Biology, MIB, The University of Manchester, Manchester M1 7DN, United Kingdom, and
| | - Nadine Veith
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,; BioQuant and
| | - Vlad Cojocaru
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Antje Sieg
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Hans V Westerhoff
- Manchester Centre for Integrative Systems Biology, MIB, The University of Manchester, Manchester M1 7DN, United Kingdom, and; Synthetic Systems Biology, SILS, the University of Amsterdam, and Molecular Cell Physiology, FALW, Netherlands Institute for Systems Biology, VU University Amsterdam, NL-1018 HV Amsterdam, The Netherlands
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Rebecca C Wade
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,; Center for Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany,.
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany,.
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43
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Steele J, Broadbent J, Kok J. Perspectives on the contribution of lactic acid bacteria to cheese flavor development. Curr Opin Biotechnol 2012; 24:135-41. [PMID: 23279928 DOI: 10.1016/j.copbio.2012.12.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/06/2012] [Accepted: 12/06/2012] [Indexed: 11/16/2022]
Abstract
It has been known since the 1960s that lactic acid bacteria are essential for the development of cheese flavor. In the ensuing 50 years significant research has been directed at understanding the microbiology, genetics and biochemistry of this process. This review briefly covers the current status of cheese flavor development and then provides our vision for approaches which will enhance our understanding of this process. The long-term goal of this area of research is to enable technology (i.e. cultures and enzymes) that results in consistent rapid development of cheese variety-specific characteristic flavors.
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Affiliation(s)
- James Steele
- University of Wisconsin-Madison, Department of Food Science, 1605 Linden Drive, Madison, WI 53706, USA
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44
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Oxaran V, Ledue-Clier F, Dieye Y, Herry JM, Péchoux C, Meylheuc T, Briandet R, Juillard V, Piard JC. Pilus biogenesis in Lactococcus lactis: molecular characterization and role in aggregation and biofilm formation. PLoS One 2012; 7:e50989. [PMID: 23236417 PMCID: PMC3516528 DOI: 10.1371/journal.pone.0050989] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 10/29/2012] [Indexed: 02/07/2023] Open
Abstract
The genome of Lactococcus lactis strain IL1403 harbors a putative pilus biogenesis cluster consisting of a sortase C gene flanked by 3 LPxTG protein encoding genes (yhgD, yhgE, and yhhB), called here pil. However, pili were not detected under standard growth conditions. Over-expression of the pil operon resulted in production and display of pili on the surface of lactococci. Functional analysis of the pilus biogenesis machinery indicated that the pilus shaft is formed by oligomers of the YhgE pilin, that the pilus cap is formed by the YhgD pilin and that YhhB is the basal pilin allowing the tethering of the pilus fibers to the cell wall. Oligomerization of pilin subunits was catalyzed by sortase C while anchoring of pili to the cell wall was mediated by sortase A. Piliated L. lactis cells exhibited an auto-aggregation phenotype in liquid cultures, which was attributed to the polymerization of major pilin, YhgE. The piliated lactococci formed thicker, more aerial biofilms compared to those produced by non-piliated bacteria. This phenotype was attributed to oligomers of YhgE. This study provides the first dissection of the pilus biogenesis machinery in a non-pathogenic Gram-positive bacterium. Analysis of natural lactococci isolates from clinical and vegetal environments showed pili production under standard growth conditions. The identification of functional pili in lactococci suggests that the changes they promote in aggregation and biofilm formation may be important for the natural lifestyle as well as for applications in which these bacteria are used.
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Affiliation(s)
- Virginie Oxaran
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | - Florence Ledue-Clier
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | - Yakhya Dieye
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | - Jean-Marie Herry
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | | | - Thierry Meylheuc
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | - Romain Briandet
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | - Vincent Juillard
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
| | - Jean-Christophe Piard
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- Agro ParisTech, UMR 1319 Micalis, Jouy-en-Josas, France
- * E-mail:
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45
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Pneumococcal carbohydrate transport: food for thought. Trends Microbiol 2012; 20:517-22. [PMID: 22959614 DOI: 10.1016/j.tim.2012.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 02/05/2023]
Abstract
Streptococcus pneumoniae relies exclusively on carbohydrates as a carbon source and devotes 30% of all transport mechanisms to carbohydrate import. Pneumococci utilize at least 32 carbohydrates in vitro. However, some proposed substrates are not human-derived, so it is unclear where they are encountered in the host niche, and other substrates remain unidentified. The majority of transporter loci are conserved, arguing against redundancy and instead for distinct roles during pathogenesis. Despite this, expression and regulation of carbohydrate transporters in vivo remain ill defined. Recent work has also demonstrated that multiple ABC transporters share an ATPase; whether this evolved for genome minimization or for transporter regulation remains unknown. Continued efforts to understand carbohydrate import may reveal novel vaccine and therapeutic targets and increase our understanding of pneumococcal pathogenesis.
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46
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Patenge N, Fiedler T, Kreikemeyer B. Common regulators of virulence in streptococci. Curr Top Microbiol Immunol 2012; 368:111-53. [PMID: 23242855 DOI: 10.1007/82_2012_295] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Streptococcal species are a diverse group of bacteria which can be found in animals and humans. Their interactions with host organisms can vary from commensal to pathogenic. Many of the pathogenic species are causative agents of severe, invasive infections in their hosts, accounting for a high burden of morbidity and mortality, associated with high economic costs in industry and health care. Among them, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus pneumoniae, and Streptococcus suis are discussed here. An environmentally stimulated and tightly controlled expression of their virulence factors is of utmost importance for their pathogenic potential. Thus, the most universal and widespread regulators from the classes of stand-alone transcriptional regulators, two-component signal transduction systems (TCS), eukaryotic-like serine/threonine kinases, and small noncoding RNAs are the topic of this chapter. The regulatory levels are reviewed with respect to function, activity, and their role in pathogenesis. Understanding of and interfering with transcriptional regulation mechanisms and networks is a promising basis for the development of novel anti-infective therapies.
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Affiliation(s)
- Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057 Rostock, Germany
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