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Lutin J, Dufrene F, Guyot P, Palme R, Achilleos C, Bouton Y, Buchin S. Microbial composition and viability of natural whey starters used in PDO Comté cheese-making. Food Microbiol 2024; 121:104521. [PMID: 38637083 DOI: 10.1016/j.fm.2024.104521] [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: 12/21/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/20/2024]
Abstract
Natural whey starters (NWS) are cultures with undefined multiple-strains species commonly used to speed up the fermentation process of cheeses. The aim of this study was to explore the diversity and the viability of Comté cheese NWS microbiota. Culture-dependent methods, i.e. plate counting and genotypic characterization, and culture-independent methods, i.e. qPCR, viability-qPCR, fluorescence microscopy and DNA metabarcoding, were combined to analyze thirty-six NWS collected in six Comté cheese factories at two seasons. Our results highlighted that NWS were dominated by Streptococcus thermophilus (ST) and thermophilic lactobacilli. These species showed a diversity of strains based on Rep-PCR. The dominance of Lactobacillus helveticus (LH) over Lactobacillus delbrueckii (LD) varied depending on the factory and the season. This highlighted two types of NWS: the type-ST/LD (LD > LH) and the type-ST/LH (LD < LH). The microbial composition varied depending on cheese factory. One factory was distinguished by its level of culturable microbial groups (ST, enterococci and yeast) and its fungi diversity. The approaches used to estimate the viability showed that most NWS cells were viable. Further investigations are needed to understand the microbial diversity of these NWS.
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Affiliation(s)
- Jade Lutin
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Franck Dufrene
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Philippe Guyot
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Romain Palme
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Christine Achilleos
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Yvette Bouton
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France.
| | - Solange Buchin
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
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You L, Jin H, Kwok LY, Lv R, Zhao Z, Bilige M, Sun Z, Liu W, Zhang H. Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem. Sci Bull (Beijing) 2023; 68:2405-2417. [PMID: 37718237 DOI: 10.1016/j.scib.2023.09.001] [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: 03/20/2023] [Revised: 05/31/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.
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Affiliation(s)
- Lijun You
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruirui Lv
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Menghe Bilige
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wenjun Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
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Wang Y, Xu X, Chen H, Yang F, Xu B, Wang K, Liu Q, Liang G, Zhang R, Jiao X, Zhang Y. Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers. BMC Genomics 2023; 24:530. [PMID: 37679681 PMCID: PMC10483869 DOI: 10.1186/s12864-023-09623-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a "generalist" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive. RESULTS In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events. CONCLUSIONS A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xiaomeng Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Kun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Qianwen Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Guixin Liang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Ruiqi Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xin'an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
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Kim E, Lee GY, Yang SM, Kim HY. Rapid and accurate on-site identification of Lactobacillus delbrueckii subspecies in dairy products using direct polymerase chain reaction with microfluidic chip. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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Mendoza RM, Kim SH, Vasquez R, Hwang IC, Park YS, Paik HD, Moon GS, Kang DK. Bioinformatics and its role in the study of the evolution and probiotic potential of lactic acid bacteria. Food Sci Biotechnol 2023; 32:389-412. [PMID: 36911331 PMCID: PMC9992694 DOI: 10.1007/s10068-022-01142-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 11/04/2022] Open
Abstract
Due to their numerous well-established applications in the food industry, there have been many studies regarding the adaptation and evolution of lactic acid bacteria (LAB) in a wide variety of hosts and environments. Progress in sequencing technology and continual decreases in its costs have led to the availability of LAB genome sequence data. Bioinformatics has been central to the extraction of valuable information from these raw genome sequence data. This paper presents the roles of bioinformatics tools and databases in understanding the adaptation and evolution of LAB, as well as the bioinformatics methods used in the initial screening of LAB for probiotic potential. Moreover, the advantages, challenges, and limitations of employing bioinformatics for these purposes are discussed.
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Affiliation(s)
- Remilyn M. Mendoza
- Department of Animal Resources Science, Dankook University, 119 Dandae-ro, Cheonan, 31116 Republic of Korea
| | - Sang Hoon Kim
- Department of Animal Resources Science, Dankook University, 119 Dandae-ro, Cheonan, 31116 Republic of Korea
| | - Robie Vasquez
- Department of Animal Resources Science, Dankook University, 119 Dandae-ro, Cheonan, 31116 Republic of Korea
| | - In-Chan Hwang
- Department of Animal Resources Science, Dankook University, 119 Dandae-ro, Cheonan, 31116 Republic of Korea
| | - Young-Seo Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 13120 Republic of Korea
| | - Hyun-Dong Paik
- Department of Food Science and Biotechnology of Animal Resource, Konkuk University, Seoul, 05029 Republic of Korea
| | - Gi-Seong Moon
- Division of Food Science and Biotechnology, Korea National University of Transportation, Jeungpyeong, 27909 Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, 119 Dandae-ro, Cheonan, 31116 Republic of Korea
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Comparative Genomics Analysis Provides New Insights into High Ethanol Tolerance of Lactiplantibacillus pentosus LTJ12, a Novel Strain Isolated from Chinese Baijiu. Foods 2022; 12:foods12010035. [PMID: 36613254 PMCID: PMC9818588 DOI: 10.3390/foods12010035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lactic acid bacteria have received a significant amount of attention due to their probiotic characteristics. The species Lactiplantibacillus plantarum and Lactiplantibacillus pentosus are genotypically closely related, and their phenotypes are so similar that they are easily confused and mistaken. In the previous study, an ethanol-resistant strain, LTJ12, isolated from the fermented grains of soy sauce aroma type baijiu in North China, was originally identified as L. plantarum through a 16S rRNA sequence analysis. Here, the genome of strain LTJ12 was further sequenced using PacBio and Illumina sequencing technology to obtain a better understanding of the metabolic pathway underlying its resistance to ethanol stress. The results showed that the genome of strain LTJ12 was composed of one circular chromosome and three circular plasmids. The genome size is 3,512,307 bp with a GC content of 46.37%, and the number of predicted coding genes is 3248. Moreover, by comparing the coding genes with the GO (Gene Ontology), COG (Cluster of Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, the functional annotation of the genome and an assessment of the metabolic pathways were performed, with the results showing that strain LTJ12 has multiple genes that may be related to alcohol metabolism and probiotic-related genes. Antibiotic resistance gene analysis showed that there were few potential safety hazards. Further, after conducting the comparative genomics analysis, it was found that strain LTJ12 is L. pentosus but not L. plantarum, but it has more functional genes than other L. pentosus strains that are mainly related to carbohydrate transport and metabolism, transcription, replication, recombination and repair, signal transduction mechanisms, defense mechanisms and cell wall/membrane/envelope biogenesis. These unique functional genes, such as gene 2754 (encodes alcohol dehydrogenase), gene 3093 (encodes gamma-D-glutamyl-meso-diaminopimelate peptidase) and some others may enhance the ethanol tolerance and alcohol metabolism of the strain. Taken together, L. pentosus LTJ12 might be a potentially safe probiotic with a high ethanol tolerance and alcohol metabolism. The findings of this study will also shed light on the accurate identification and rational application of the Lactiplantibacillus species.
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Sola L, Quadu E, Bortolazzo E, Bertoldi L, Randazzo CL, Pizzamiglio V, Solieri L. Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait. Sci Rep 2022; 12:17322. [PMID: 36243881 PMCID: PMC9569347 DOI: 10.1038/s41598-022-22207-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.
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Affiliation(s)
- Laura Sola
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Emanuele Quadu
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Elena Bortolazzo
- grid.423913.eCentro Ricerche Produzioni Animali, 42121 Reggio Emilia, Italy
| | | | - Cinzia L. Randazzo
- grid.8158.40000 0004 1757 1969Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy ,ProBioEtna Srl, 95123 Catania, Italy
| | - Valentina Pizzamiglio
- grid.433295.aConsorzio del Formaggio Parmigiano Reggiano, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy ,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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Dai W, Gui L, Du H, Li S, Wu R. The association of cervicovaginal Langerhans cells with clearance of human papillomavirus. Front Immunol 2022; 13:918190. [PMID: 36311788 PMCID: PMC9596771 DOI: 10.3389/fimmu.2022.918190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/27/2022] [Indexed: 12/03/2022] Open
Abstract
Human papillomavirus (HPV) clearance is important in eliminating cervical cancer which contributes to high morbidity and mortality in women. Nevertheless, it remains largely unknown about key players in clearing pre-existing HPV infections. HPV antigens can be detected by the most important cervical antigen-presenting cells (Langerhans cells, LCs), of which the activities can be affected by cervicovaginal microbiota. In this review, we first introduce persistent HPV infections and then describe HPV-suppressed LCs activities, including but not limited to antigen uptake and presentation. Given specific transcriptional profiling of LCs in cervical epithelium, we also discuss the impact of cervicovaginal microbiota on LCs activation as well as the promise of exploring key microbial players in activating LCs and HPV-specific cellular immunity.
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Affiliation(s)
- Wenkui Dai
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Liming Gui
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Hui Du
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Shuaicheng Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ruifang Wu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
- *Correspondence: Ruifang Wu,
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Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
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Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
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10
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Guo C, Dai W, Zhou Q, Gui L, Cai H, Wu D, Hou J, Li C, Li S, Du H, Wu R. Cervicovaginal microbiota significantly changed for HPV-positive women with high-grade squamous intraepithelial lesion. Front Cell Infect Microbiol 2022; 12:973875. [PMID: 35992171 PMCID: PMC9386141 DOI: 10.3389/fcimb.2022.973875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Lower female genital tract is colonized by a variety of microbes (cervicovaginal microbiota, CVM) which associate with the risk of genital infection. This study characterized CVM for 149 Chinese women with different status of human papillomavirus (HPV) infection and squamous intraepithelial lesion (SIL): no HPV infection (HPV-), HPV infection without significant SIL (HPV+NoSIL), HPV infection with low-grade SIL (HPV+LSIL) and HPV infection with high-grade SIL (HPV+HSIL). Analysis results showed CVM has dramatically changed in HPV+HSIL group when compared to HPV+LSIL group, but it exhibited no significant differences between HPV- and HPV+NoSIL groups as well as between HPV+NoSIL and HPV+LSIL groups. In consistence, random forest analysis found more notable differences in HPV+HSIL vs HPV+LSIL comparison than in other comparisons. In addition, depletion of Lactobacillus in CVM was more to be frequently identified in SIL-positive women as compared to SIL-negative individuals. Our findings suggested that significant CVM differences occurred when SIL developed to HSIL which was caused by persistent HPV infection.
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Affiliation(s)
- Chunlei Guo
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Wenkui Dai
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Qian Zhou
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Liming Gui
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Han Cai
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Di Wu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jun Hou
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Changzhong Li
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hui Du
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
- *Correspondence: Ruifang Wu, ; Hui Du,
| | - Ruifang Wu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center (PKU-HKUST) Medical Center, Shenzhen, China
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
- *Correspondence: Ruifang Wu, ; Hui Du,
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11
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Wani AK, Roy P, Kumar V, Mir TUG. Metagenomics and artificial intelligence in the context of human health. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105267. [PMID: 35278679 DOI: 10.1016/j.meegid.2022.105267] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/12/2022]
Abstract
Human microbiome is ubiquitous, dynamic, and site-specific consortia of microbial communities. The pathogenic nature of microorganisms within human tissues has led to an increase in microbial studies. Characterization of genera, like Streptococcus, Cutibacterium, Staphylococcus, Bifidobacterium, Lactococcus and Lactobacillus through culture-dependent and culture-independent techniques has been reported. However, due to the unique environment within human tissues, it is difficult to culture these microorganisms making their molecular studies strenuous. MGs offer a gateway to explore and characterize hidden microbial communities through a culture-independent mode by direct DNA isolation. By function and sequence-based MGs, Scientists can explore the mechanistic details of numerous microbes and their interaction with the niche. Since the data generated from MGs studies is highly complex and multi-dimensional, it requires accurate analytical tools to evaluate and interpret the data. Artificial intelligence (AI) provides the luxury to automatically learn the data dimensionality and ease its complexity that makes the disease diagnosis and disease response easy, accurate and timely. This review provides insight into the human microbiota and its exploration and expansion through MG studies. The review elucidates the significance of MGs in studying the changing microbiota during disease conditions besides highlighting the role of AI in computational analysis of MG data.
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Affiliation(s)
- Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Priyanka Roy
- Department of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Sonipat 131 028, Haryana, India
| | - Vijay Kumar
- Department of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Sonipat 131 028, Haryana, India.
| | - Tahir Ul Gani Mir
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
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12
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 PMCID: PMC8776748 DOI: 10.1038/s41396-021-01071-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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13
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 DOI: 10.1101/2021.01.14.426499v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 05/27/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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14
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Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
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15
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Shani N, Oberhaensli S, Berthoud H, Schmidt RS, Bachmann HP. Antimicrobial Susceptibility of Lactobacillus delbrueckii subsp. lactis from Milk Products and Other Habitats. Foods 2021; 10:foods10123145. [PMID: 34945696 PMCID: PMC8701367 DOI: 10.3390/foods10123145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
As components of many cheese starter cultures, strains of Lactobacillus delbrueckii subsp. lactis (LDL) must be tested for their antimicrobial susceptibility to avoid the potential horizontal transfer of antibiotic resistance (ABR) determinants in the human body or in the environment. To this end, a phenotypic test, as well as a screening for antibiotic resistance genes (ARGs) in genome sequences, is commonly performed. Historically, microbiological cutoffs (MCs), which are used to classify strains as either 'sensitive' or 'resistant' based on the minimal inhibitory concentrations (MICs) of a range of clinically-relevant antibiotics, have been defined for the whole group of the obligate homofermentative lactobacilli, which includes LDL among many other species. This often leads to inaccuracies in the appreciation of the ABR status of tested LDL strains and to false positive results. To define more accurate MCs for LDL, we analyzed the MIC profiles of strains originating from various habitats by using the broth microdilution method. These strains' genomes were sequenced and used to complement our analysis involving a search for ARGs, as well as to assess the phylogenetic proximity between strains. Of LDL strains, 52.1% displayed MICs that were higher than the defined MCs for kanamycin, 9.9% for chloramphenicol, and 5.6% for tetracycline, but no ARG was conclusively detected. On the other hand, all strains displayed MICs below the defined MCs for ampicillin, gentamycin, erythromycin, and clindamycin. Considering our results, we propose the adaptation of the MCs for six of the tested clinically-relevant antibiotics to improve the accuracy of phenotypic antibiotic testing.
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Affiliation(s)
- Noam Shani
- Competence Division Methods Development and Analytics, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland;
- Correspondence:
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland;
| | - Hélène Berthoud
- Competence Division Methods Development and Analytics, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland;
| | - Remo S. Schmidt
- Research Division Food Microbial Systems, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; (R.S.S.); (H.-P.B.)
| | - Hans-Peter Bachmann
- Research Division Food Microbial Systems, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; (R.S.S.); (H.-P.B.)
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16
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Mancini A, Rodriguez MC, Zago M, Cologna N, Goss A, Carafa I, Tuohy K, Merz A, Franciosi E. Massive Survey on Bacterial-Bacteriophages Biodiversity and Quality of Natural Whey Starter Cultures in Trentingrana Cheese Production. Front Microbiol 2021; 12:678012. [PMID: 34194413 PMCID: PMC8236940 DOI: 10.3389/fmicb.2021.678012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
This study focused on the microbial and bacteriophages identification and characterization in cheese-production facilities that use natural whey starter (NWS) cultures for Trentingrana production. Bacterial and phage screening was carried out on cooked not acidified whey and NWS samples isolated from six dairy factories, for 4 consecutive days in four different months. By means of a combined approach, using plate counts, bacterial isolation, and metataxonomic analysis Lactobacillus helveticus was found occurring as the dominant species in NWS cultures and Levilactobacillus brevis as codominant in the cheese factories where the temperature of NWS production was mainly lower than 40°C, suggesting that the variability in the parameters of the NWS culture preparation could differently modulate the bacterial species in NWS cultures. Using turbidity test approach on 303 bacterial isolates from the NWS cultures, 120 distinct phages were identified. L. helveticus phage contamination of NWS cultures was revealed in most of the analyzed samples, but despite the great recovery of bacteriophage contamination cases, the microbial quality of NWS cultures was high. Our results support the presence of natural bacteriophage resistance mechanisms in L. helveticus. The use of NWS cultures probably creates an ideal environment for the proliferation of different L. helveticus strains balanced with their phages without a clear dominance. It is evident, from this study, that the presence of a high biodiversity of NWS bacterial strains is relevant to avoid phages dominance in NWS cultures and consequently to keep a good acidification ability.
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Affiliation(s)
- Andrea Mancini
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Maria Cid Rodriguez
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Miriam Zago
- Centro di ricerca Zootecnia e Acquacoltura (CREA-ZA), Lodi, Italy
| | - Nicola Cologna
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Andrea Goss
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Ilaria Carafa
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Kieran Tuohy
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Andrea Merz
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Elena Franciosi
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
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17
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Gustaw K, Koper P, Polak-Berecka M, Rachwał K, Skrzypczak K, Waśko A. Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead. Int J Mol Sci 2021; 22:ijms22073780. [PMID: 33917427 PMCID: PMC8038741 DOI: 10.3390/ijms22073780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022] Open
Abstract
The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. L. hilgardii FLUB possesses three clustered regularly interspaced short palindromic repeats (CRISPR), eight genomic islands (44,155 bp to 6345 bp), and three (two intact and one incomplete) prophage regions. For the first time, the characteristics of the genome of this species were described and a pangenomic analysis was performed. The concept of the pangenome was used not only to establish the genetic repertoire of this species, but primarily to highlight the unique characteristics of L. hilgardii FLUB. The core of the genome of L. hilgardii is centered around genes related to the storage and processing of genetic information, as well as to carbohydrate and amino acid metabolism. Strains with such a genetic constitution can effectively adapt to environmental changes. L. hilgardii FLUB is distinguished by an extensive cluster of metabolic genes, arsenic detoxification genes, and unique surface layer proteins. Variants of MRS broth with ethanol (10-20%), glucose (2-25%), and fructose (2-24%) were prepared to test the strain's growth preferences using Bioscreen C and the PYTHON script. L. hilgardii FLUB was found to be more resistant than a reference strain to high concentrations of alcohol (18%) and sugars (25%). It exhibited greater preference for fructose than glucose, which suggests it has a fructophilic nature. Comparative genomic analysis supported by experimental research imitating the conditions of alcoholic beverages confirmed the niche specialization of L. hilgardii FLUB to the mead environment.
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Affiliation(s)
- Klaudia Gustaw
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland; (M.P.-B.); (K.R.); (A.W.)
- Correspondence: (K.G.); (P.K.)
| | - Piotr Koper
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
- Correspondence: (K.G.); (P.K.)
| | - Magdalena Polak-Berecka
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland; (M.P.-B.); (K.R.); (A.W.)
| | - Kamila Rachwał
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland; (M.P.-B.); (K.R.); (A.W.)
| | - Katarzyna Skrzypczak
- Department of Fruits, Vegetables and Mushrooms Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland;
| | - Adam Waśko
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland; (M.P.-B.); (K.R.); (A.W.)
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18
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Qi Y, Jiang Y, Zhang X, Lee YK, Liu X, Zhao J, Zhang H, Chen W. Diversity in genetic and peptidase activity of Lactobacillus helveticus strains biodiversity of Lactobacillus helveticus. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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19
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Kido Y, Maeno S, Tanno H, Kichise Y, Shiwa Y, Endo A. Niche-specific adaptation of Lactobacillus helveticus strains isolated from malt whisky and dairy fermentations. Microb Genom 2021; 7:000560. [PMID: 33900907 PMCID: PMC8208680 DOI: 10.1099/mgen.0.000560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/15/2021] [Indexed: 01/24/2023] Open
Abstract
Lactobacillus helveticus is a well characterized lactobacillus for dairy fermentations that is also found in malt whisky fermentations. The two environments contain considerable differences related to microbial growth, including the presence of different growth inhibitors and nutrients. The present study characterized L. helveticus strains originating from dairy fermentations (called milk strains hereafter) and malt whisky fermentations (called whisky strains hereafter) by in vitro phenotypic tests and comparative genomics. The whisky strains can tolerate ethanol more than the milk strains, whereas the milk strains can tolerate lysozyme and lactoferrin more than the whisky strains. Several plant-origin carbohydrates, including cellobiose, maltose, sucrose, fructooligosaccharide and salicin, were generally metabolized only by the whisky strains, whereas milk-derived carbohydrates, i.e. lactose and galactose, were metabolized only by the milk strains. Milk fermentation properties also distinguished the two groups. The general genomic characteristics, including genomic size, number of coding sequences and average nucleotide identity values, differentiated the two groups. The observed differences in carbohydrate metabolic properties between the two groups correlated with the presence of intact specific enzymes in glycoside hydrolase (GH) families GH1, GH4, GH13, GH32 and GH65. Several GHs in the milk strains were inactive due to the presence of stop codon(s) in genes encoding the GHs, and the inactivation patterns of the genes encoding specific enzymes assigned to GH1 in the milk strains suggested a possible diversification manner of L. helveticus strains. The present study has demonstrated how L. helveticus strains have adapted to their habitats.
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Affiliation(s)
- Yoshihiko Kido
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Hiroki Tanno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Yuko Kichise
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
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20
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Walther B, Guggisberg D, Schmidt RS, Portmann R, Risse MC, Badertscher R, Chollet M. Quantitative analysis of menaquinones (vitamin K2) in various types of cheese from Switzerland. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2020.104853] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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21
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Varadarajan AR, Allan RN, Valentin JDP, Castañeda Ocampo OE, Somerville V, Pietsch F, Buhmann MT, West J, Skipp PJ, van der Mei HC, Ren Q, Schreiber F, Webb JS, Ahrens CH. An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1. NPJ Biofilms Microbiomes 2020; 6:46. [PMID: 33127897 PMCID: PMC7603352 DOI: 10.1038/s41522-020-00154-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms.
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Affiliation(s)
- Adithi R Varadarajan
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Raymond N Allan
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- National Biofilms Innovation Centre, University of Southampton, Southampton, SO17 1BJ, UK
- School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH, UK
| | - Jules D P Valentin
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Olga E Castañeda Ocampo
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Vincent Somerville
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Franziska Pietsch
- Division of Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Matthias T Buhmann
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Jonathan West
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Hybrid Biodevices, University of Southampton, Southampton, SO17 1BJ, UK
| | - Paul J Skipp
- Centre for Proteomics Research, University of Southampton, Southampton, SO17 1BJ, UK
| | - Henny C van der Mei
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Qun Ren
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Jeremy S Webb
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- National Biofilms Innovation Centre, University of Southampton, Southampton, SO17 1BJ, UK
| | - Christian H Ahrens
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
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22
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Zhong Z, Hu R, Zhao J, Liu W, Kwok LY, Sun Z, Zhang H, Chen Y. Acetate kinase and peptidases are associated with the proteolytic activity of Lactobacillus helveticus isolated from fermented food. Food Microbiol 2020; 94:103651. [PMID: 33279076 DOI: 10.1016/j.fm.2020.103651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 11/18/2022]
Abstract
Lactobacillus (L.) helveticus is widely used in food industry due to its high proteolytic activity. However, such activity varies greatly between isolates, and the determining factors regulating the strength of proteolytic activity in L. helveticus are unclear. This study sequenced the genomes of 60 fermented food-originated L. helveticus and systemically examined the proteolytic activity-determining factors. Our analyses found that the strength of proteolytic activity in L. helveticus was independent of the isolation source, geographic location, phylogenetic closeness between isolates, and distribution of cell envelope proteinases (CEPs). Genome-wide association study (GWAS) identified two genes, the acetate kinase (ackA) and a hypothetical protein, and 15 single nucleotide polymorphisms (SNPs) that were associated with the strength of the proteolytic activity. Further investigating the functions of these gene components revealed that ackA and two cysteine peptidases coding genes (pepC and srtA) rather than the highly heterogeneous and intraspecific CEPs were linked to the level of proteolytic activity. Moreover, the sequence type (ST) defined by SNP analysis revealed a total of ten STs, and significantly weaker proteolytic activity was observed among isolates of ST2. This study provides practical information for future selection of L. helveticus of strong proteolytic activity.
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Affiliation(s)
- Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Richa Hu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jie Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.
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23
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Pintara A, Jennison A, Rathnayake IU, Mellor G, Huygens F. Core and Accessory Genome Comparison of Australian and International Strains of O157 Shiga Toxin-Producing Escherichia coli. Front Microbiol 2020; 11:566415. [PMID: 33013798 PMCID: PMC7498637 DOI: 10.3389/fmicb.2020.566415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australian STEC epidemiology differs from many other countries, as severe outbreaks and HUS cases appear to be more often associated with non-O157 serogroups. It is not known why Australian strains of O157 STEC might differ in virulence to international strains. Here we investigate the reduced virulence of Australian strains. Multiple genetic analyses were performed, including SNP-typing, to compare the core genomes of the Australian to the international isolates, and accessory genome analysis to determine any significant differences in gene presence/absence that could be associated with their phenotypic differences in virulence. The most distinct difference between the isolates was the absence of the stx2a gene in all Australian isolates, with few other notable differences observed in the core and accessory genomes of the O157 STEC isolates analyzed in this study. The presence of stx1a in most Australian isolates was another notable observation. Acquisition of stx2a seems to coincide with the emergence of highly pathogenic STEC. Due to the lack of other notable genotypic differences observed between Australian and international isolates characterized as highly pathogenic, this may be further evidence that the absence of stx2a in Australian O157 STEC could be a significant characteristic defining its mild virulence. Further work investigating the driving force(s) behind Stx prophage loss and acquisition is needed to determine if this potential exists in Australian O157 isolates.
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Affiliation(s)
- Alexander Pintara
- Centre for Immunology and Infection Control, Queensland University of Technology, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Amy Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, QLD, Australia
| | - Irani U. Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, QLD, Australia
| | - Glen Mellor
- CSIRO Animal, Food and Health Sciences, Archerfield, QLD, Australia
| | - Flavia Huygens
- Centre for Immunology and Infection Control, Queensland University of Technology, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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24
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Miragoli F, Patrone V, Romaniello F, Rebecchi A, Callegari ML. Development of an S-layer gene-based PCR-DGGE assay for monitoring dominant Lactobacillus helveticus strains in natural whey starters of Grana Padano cheese. Food Microbiol 2020; 89:103457. [DOI: 10.1016/j.fm.2020.103457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/11/2019] [Accepted: 02/08/2020] [Indexed: 10/25/2022]
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25
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De Vrieze M, Varadarajan AR, Schneeberger K, Bailly A, Rohr RP, Ahrens CH, Weisskopf L. Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight. Front Microbiol 2020; 11:857. [PMID: 32425922 PMCID: PMC7204214 DOI: 10.3389/fmicb.2020.00857] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/09/2020] [Indexed: 01/22/2023] Open
Abstract
For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction of abiotic and biotic stresses and enhanced protection against various pests and diseases. Beneficial bacteria rightly equipped for successful plant colonization and showing antagonistic activity toward plant pathogens seem to be actively recruited by plants. To gain more insights into the genetic determinants responsible for plant colonization and antagonistic activities, we first sequenced and de novo assembled the complete genomes of nine Pseudomonas strains that had exhibited varying antagonistic potential against the notorious oomycete Phytophthora infestans, placed them into the phylogenomic context of known Pseudomonas biocontrol strains and carried out a comparative genomic analysis to define core, accessory (i.e., genes found in two or more, but not all strains) and unique genes. Next, we assessed the colonizing abilities of these strains and used bioassays to characterize their inhibitory effects against different stages of P. infestans' lifecycle. The phenotype data were then correlated with genotype information, assessing over three hundred genes encoding known factors for plant colonization and antimicrobial activity as well as secondary metabolite biosynthesis clusters predicted by antiSMASH. All strains harbored genes required for successful plant colonization but also distinct arsenals of antimicrobial compounds. We identified genes coding for phenazine, hydrogen cyanide, 2-hexyl, 5-propyl resorcinol and pyrrolnitrin synthesis, as well as various siderophores, pyocins and type VI secretion systems. Additionally, the comparative genomic analysis revealed about a hundred accessory genes putatively involved in anti-Phytophthora activity, including a type II secretion system (T2SS), several peptidases and a toxin. Transcriptomic studies and mutagenesis are needed to further investigate the putative involvement of the novel candidate genes and to identify the various mechanisms involved in the inhibition of P. infestans by different Pseudomonas strains.
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Affiliation(s)
- Mout De Vrieze
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Adithi R. Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Kerstin Schneeberger
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Rudolf P. Rohr
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Christian H. Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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26
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Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships. J Proteome Res 2020; 19:1647-1662. [PMID: 32091902 DOI: 10.1021/acs.jproteome.9b00842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal foodborne disease. Many different Listeria strains and serotypes exist, but a proteogenomic resource that bridges the gap in our molecular understanding of the relationships between the Listeria genotypes and phenotypes via proteotypes is still missing. Here, we devised a next-generation proteogenomics strategy that enables the community to rapidly proteotype Listeria strains and relate this information back to the genotype. Based on sequencing and de novo assembly of the two most commonly used Listeria model strains, EGD-e and ScottA, we established two comprehensive Listeria proteogenomic databases. A genome comparison established core- and strain-specific genes potentially responsible for virulence differences. Next, we established a DIA/SWATH-based proteotyping strategy, including a new and robust sample preparation workflow, that enables the reproducible, sensitive, and relative quantitative measurement of Listeria proteotypes. This reusable and publicly available DIA/SWATH library covers 70% of open reading frames of Listeria and represents the most extensive spectral library for Listeria proteotype analysis to date. We used these two new resources to investigate the Listeria proteotype in states mimicking the upper gastrointestinal passage. Exposure of Listeria to bile salts at 37 °C, which simulates conditions encountered in the duodenum, showed significant proteotype perturbations including an increase of FlaA, the structural protein of flagella. Given that Listeria is known to lose its flagella above 30 °C, this was an unexpected finding. The formation of flagella, which might have implications on infectivity, was validated by parallel reaction monitoring and light and scanning electron microscopy. flaA transcript levels did not change significantly upon exposure to bile salts at 37 °C, suggesting regulation at the post-transcriptional level. Together, these analyses provide a comprehensive proteogenomic resource and toolbox for the Listeria community enabling the analysis of Listeria genotype-proteotype-phenotype relationships.
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Affiliation(s)
- Adithi R Varadarajan
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, 8820 Wädenswil, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
| | - Maria P Pavlou
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
| | - Virginie Grosboillot
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Yang Shen
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Martin J Loessner
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, 8820 Wädenswil, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
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27
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Guo L, Dai Z, Guo J, Yang W, Ge F, Dai Y. Oligotrophic bacterium Hymenobacter latericoloratus CGMCC 16346 degrades the neonicotinoid imidacloprid in surface water. AMB Express 2020; 10:7. [PMID: 31939001 PMCID: PMC6960279 DOI: 10.1186/s13568-019-0942-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 12/26/2019] [Indexed: 02/06/2023] Open
Abstract
The intensive and extensive application of imidacloprid in agriculture has resulted in water pollution and risks to aquatic invertebrates. However, pure bacteria remediation of imidacloprid in surface water environments has not been studied. Here, we isolated an imidacloprid-degrading bacterium from a water environment, examined its imidacloprid degradation in pure culture and surface water, sequenced its genome, and compared its Clusters of Orthologous Groups (COG) protein categorization with that for another imidacloprid-degrading bacterium. The isolate was an obligate oligotrophic bacterium, Hymenobacter latericoloratus CGMCC 16346, which degraded imidacloprid via hydroxylation by co-metabolism in pure culture. Resting cells degraded 64.4% of 100 mg/L imidacloprid in 6 days in the presence of co-substrate maltose, and growing culture degraded 40.8% of imidacloprid in 10 days. H. latericoloratus CGMCC 16346 degraded imidacloprid in surface water without co-substrate supplementation and retained imidacloprid-degrading activity after 30 days. The half-life of imidacloprid in surface water was decreased from 173.3 days in the control to 57.8 days by CGMCC 16346 inoculation. Genome sequencing and COG analysis indicated that carbohydrate metabolism and transport, cell wall/membrane biogenesis, and defense mechanisms are enriched in H. latericoloratus CGMCC 16346 compared with the copiotrophic imidacloprid-degrading Pseudoxanthomonas indica CGMCC 6648, indicating that H. latericoloratus CGMCC 16346 is adapted to live in oligotrophic water environments and biofilms. H. latericoloratus CGMCC 16346 is a promising bioremediation agent for elimination of imidacloprid contamination from surface water.
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28
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Draft Genome Sequences of Six Lactobacillus gasseri and Three Lactobacillus paragasseri Strains Isolated from the Female Bladder. Microbiol Resour Announc 2019; 8:8/37/e00973-19. [PMID: 31515350 PMCID: PMC6742801 DOI: 10.1128/mra.00973-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Lactobacilli are dominant members of the healthy female bladder microbiota. Here, we report the complete genome sequences of six Lactobacillus gasseri and three Lactobacillus paragasseri strains isolated from catheterized urine samples. These L. paragasseri genomes are the first publicly available sequences of the species from the bladder. Lactobacilli are dominant members of the healthy female bladder microbiota. Here, we report the complete genome sequences of six Lactobacillus gasseri and three Lactobacillus paragasseri strains isolated from catheterized urine samples. These L. paragasseri genomes are the first publicly available sequences of the species from the bladder.
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29
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Draft Genome Sequences of 11 Lactobacillus jensenii Strains Isolated from the Female Bladder. Microbiol Resour Announc 2019; 8:8/35/e00970-19. [PMID: 31467111 PMCID: PMC6715881 DOI: 10.1128/mra.00970-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Lactobacillus jensenii, a protective bacterium in the vaginal microbiota, is also a member of the female urinary tract community. Here, we report 11 genome sequences of L. jensenii strains isolated from catheterized urine from women. This effort greatly increases our knowledge of the genetic diversity of this species within the bladder.
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30
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Almeida EL, Carrillo Rincón AF, Jackson SA, Dobson ADW. Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential. Front Microbiol 2019; 10:1713. [PMID: 31404169 PMCID: PMC6676996 DOI: 10.3389/fmicb.2019.01713] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/11/2019] [Indexed: 12/28/2022] Open
Abstract
The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.
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Affiliation(s)
| | | | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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31
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Fontana A, Falasconi I, Molinari P, Treu L, Basile A, Vezzi A, Campanaro S, Morelli L. Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential. Front Microbiol 2019; 10:1380. [PMID: 31293536 PMCID: PMC6606699 DOI: 10.3389/fmicb.2019.01380] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/03/2019] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-β-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Irene Falasconi
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paola Molinari
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Laura Treu
- Department of Biology, University of Padua, Padua, Italy
| | - Arianna Basile
- Department of Biology, University of Padua, Padua, Italy
| | | | - Stefano Campanaro
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP, Ahrens CH. Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Res 2019; 46:8953-8965. [PMID: 30137508 PMCID: PMC6158609 DOI: 10.1093/nar/gky726] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also included a variable shufflon region, could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from Oxford Nanopore Technologies. Importantly, a repeat analysis, whose results we release for over 9600 prokaryotes, indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this ‘dark matter’ for de novo genome assembly of prokaryotes. Several of these ‘dark matter’ genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assembly algorithms capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.
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Affiliation(s)
- Michael Schmid
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, University of Zurich & ETH Zurich, Zurich CH-8057, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich & ETH Zurich, Zurich CH-8057, Switzerland
| | - Jürg E Frey
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil CH-8820, Switzerland
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Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. BMC Microbiol 2019; 19:143. [PMID: 31238873 PMCID: PMC6593500 DOI: 10.1186/s12866-019-1500-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/31/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS Two NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.
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Affiliation(s)
- Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Daniel Frei
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Jürg E. Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Christian H. Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
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34
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Gan HM, Lee MVL, Savka MA. Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 2019; 7:e6366. [PMID: 30775173 PMCID: PMC6369824 DOI: 10.7717/peerj.6366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Melvin V L Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Michael A Savka
- College of Science, The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
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Terán LC, Coeuret G, Raya R, Zagorec M, Champomier-Vergès MC, Chaillou S. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome Biol Evol 2018; 10:1516-1525. [PMID: 29850855 PMCID: PMC6007345 DOI: 10.1093/gbe/evy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
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Affiliation(s)
- Lucrecia C Terán
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Gwendoline Coeuret
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Raúl Raya
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | | | - Stéphane Chaillou
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
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36
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McAuliffe O, Kilcawley K, Stefanovic E. Symposium review: Genomic investigations of flavor formation by dairy microbiota. J Dairy Sci 2018; 102:909-922. [PMID: 30343908 DOI: 10.3168/jds.2018-15385] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 08/24/2018] [Indexed: 01/15/2023]
Abstract
Flavor is one of the most important attributes of any fermented dairy product. Dairy consumers are known to be willing to experiment with different flavors; thus, many companies producing fermented dairy products have looked at culture manipulation as a tool for flavor diversification. The development of flavor is a complex process, originating from a combination of microbiological, biochemical, and technological aspects. A key driver of flavor is the enzymatic activities of the deliberately inoculated starter cultures, in addition to the environmental or "nonstarter" microbiota. The contribution of microbial metabolism to flavor development in fermented dairy products has been exploited for thousands of years, but the availability of the whole genome sequences of the bacteria and yeasts involved in the fermentation process and the possibilities now offered by next-generation sequencing and downstream "omics" technologies is stimulating a more knowledge-based approach to the selection of desirable cultures for flavor development. By linking genomic traits to phenotypic outputs, it is now possible to mine the metabolic diversity of starter cultures, analyze the metabolic routes to flavor compound formation, identify those strains with flavor-forming potential, and select them for possible commercial application. This approach also allows for the identification of species and strains not previously considered as potential flavor-formers, the blending of strains with complementary metabolic pathways, and the potential improvement of key technological characteristics in existing strains, strains that are at the core of the dairy industry. An in-depth knowledge of the metabolic pathways of individual strains and their interactions in mixed culture fermentations can allow starter blends to be custom-made to suit industry needs. Applying this knowledge to starter culture research programs is enabling research and development scientists to develop superior starters, expand flavor profiles, and potentially develop new products for future market expansion.
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Affiliation(s)
- Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996.
| | - Kieran Kilcawley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - Ewelina Stefanovic
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
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37
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The effect of starters with a functional arginine deiminase pathway on cheese ripening and quality. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Linezolid resistance genes and genetic elements enhancing their dissemination in enterococci and streptococci. Plasmid 2018; 99:89-98. [PMID: 30253132 DOI: 10.1016/j.plasmid.2018.09.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023]
Abstract
Linezolid is considered a last resort drug in treatment of severe infections caused by Gram-positive pathogens, resistant to other antibiotics, such as vancomycin-resistant enterococci (VRE), methicillin-resistant staphylococci and multidrug resistant pneumococci. Although the vast majority of Gram-positive pathogenic bacteria remain susceptible to linezolid, resistant isolates of enterococci, staphylococci and streptococci have been reported worldwide. In these bacteria, apart from mutations, affecting mostly the 23S rRNA genes, acquisition of such genes as cfr, cfr(B), optrA and poxtA, often associated with mobile genetic elements (MGE), plays an important role for resistance. The purpose of this paper is to provide an overview on diversity and epidemiology of MGE carrying linezolid-resistance genes among clinically-relevant Gram-positive pathogens such as enterococci and streptococci.
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39
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Crawley AB, Barrangou R. Conserved Genome Organization and Core Transcriptome of the Lactobacillus acidophilus Complex. Front Microbiol 2018; 9:1834. [PMID: 30150974 PMCID: PMC6099100 DOI: 10.3389/fmicb.2018.01834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/23/2018] [Indexed: 01/08/2023] Open
Abstract
The Lactobacillus genus encompasses a genetically and functionally diverse group of species, and contains many strains widely formulated in the human food supply chain as probiotics and starter cultures. Within this genetically expansive group, there are several distinct clades that have high levels of homology, one of which is the Lactobacillus acidophilus group. Of the uniting features, small genomes, low GC content, adaptation to dairy environments, and fastidious growth requirements, are some of the most defining characteristics of this group. To better understand what truly links and defines this clade, we sought to characterize the genomic organization and content of the genomes of several members of this group. Through core genome analysis we explored the synteny and intrinsic genetic underpinnings of the L. acidophilus clade, and observed key features related to the evolution and adaptation of these organisms. While genetic content is able to provide a large map of the potential of each organism, it does not always reflect their functionality. Through transcriptomic data we inferred the core transcriptome of the L. acidophilus complex to better define the true metabolic capabilities that unite this clade. Using this approach we have identified seven small ORFs that are both highly conserved and transcribed in diverse members of this clade and could be potential novel small peptide or untranslated RNA regulators. Overall, our results reveal the core features of the L. acidophilus complex and open new avenues for the enhancement and formulation and of next generation probiotics and starter cultures.
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Affiliation(s)
- Alexandra B Crawley
- Genomic Sciences Program, NC State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, NC State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Program, NC State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, NC State University, Raleigh, NC, United States
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40
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Moser A, Schafroth K, Meile L, Egger L, Badertscher R, Irmler S. Population Dynamics of Lactobacillus helveticus in Swiss Gruyère-Type Cheese Manufactured With Natural Whey Cultures. Front Microbiol 2018; 9:637. [PMID: 29670601 PMCID: PMC5893823 DOI: 10.3389/fmicb.2018.00637] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus helveticus, a ubiquitous bacterial species in natural whey cultures (NWCs) used for Swiss Gruyère cheese production, is considered to have crucial functions for cheese ripening such as enhancing proteolysis. We tracked the diversity and abundance of L. helveticus strains during 6 months of ripening in eight Swiss Gruyère-type cheeses using a culture-independent typing method. The study showed that the L. helveticus population present in NWCs persisted in cheese and demonstrated a stable multi-strain coexistence during cheese ripening. With regard to proteolysis, one of the eight L. helveticus populations exhibited less protein degradation during ripening.
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Affiliation(s)
- Aline Moser
- Agroscope, Bern, Switzerland.,Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | | | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
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