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Konno N, Maeno S, Tanizawa Y, Arita M, Endo A, Iwasaki W. Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments. Commun Biol 2024; 7:902. [PMID: 39048718 PMCID: PMC11269746 DOI: 10.1038/s42003-024-06580-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
Convergence provides clues to unveil the non-random nature of evolution. Intermediate paths toward convergence inform us of the stochasticity and the constraint of evolutionary processes. Although previous studies have suggested that substantial constraints exist in microevolutionary paths, it remains unclear whether macroevolutionary convergence follows stochastic or constrained paths. Here, we performed comparative genomics for hundreds of lactic acid bacteria (LAB) species, including clades showing a convergent gene repertoire and sharing fructose-rich habitats. By adopting phylogenetic comparative methods we showed that the genomic convergence of distinct fructophilic LAB (FLAB) lineages was caused by parallel losses of more than a hundred orthologs and the gene losses followed significantly similar orders. Our results further suggested that the loss of adhE, a key gene for phenotypic convergence to FLAB, follows a specific evolutionary path of domain architecture decay and amino acid substitutions in multiple LAB lineages sharing fructose-rich habitats. These findings unveiled the constrained evolutionary paths toward the convergence of free-living bacterial clades at the genomic and molecular levels.
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Affiliation(s)
- Naoki Konno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Shintaro Maeno
- Research Center for Advance Science and Innovation Organization for Research Initiatives, Yamaguchi University, Yamaguchi, Yamaguchi, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Akihito Endo
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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He X, Yu Y, Kemperman R, Jimenez L, Ahmed Sadiq F, Zhang G. Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains. Microorganisms 2024; 12:845. [PMID: 38792675 PMCID: PMC11124214 DOI: 10.3390/microorganisms12050845] [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: 04/08/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. In this research, 14 F. sanfranciscensis strains were isolated from sourdough samples to evaluate the genetic diversity and variation in metabolic traits. These 14 and 31 other strains (obtained from the NCBI database) genomes were compared. The values for genome size and GC content, on average, turned out to 1.31 Mbp and 34.25%, respectively. In 45 F. sanfranciscensis strains, there were 162 core genes and 0 to 51 unique genes present in each strain. The primary functions of core genes were related to nucleotide, lipid transport, and amino acid, as well as carbohydrate metabolism. The size of core genes accounted for 41.18% of the pan-genome size in 14 F. sanfranciscensis strains, i.e., 0.70 Mbp of 1.70 Mbp. There were genetic variations among the 14 strains involved in carbohydrate utilization and antibiotic resistance. Moreover, exopolysaccharides biosynthesis-related genes were annotated, including epsABD, wxz, wzy. The Type IIA & IE CRISPR-Cas systems, pediocin PA-1 and Lacticin_3147_A1 bacteriocins operons were also discovered in F. sanfranciscensis. These findings can help to select desirable F. sanfranciscensis strains to develop standardized starter culture for sourdough fermentation, and expect to provide traditional fermented pasta with a higher quality and nutritional value for the consumers.
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Affiliation(s)
- Xiaxia He
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.H.); (Y.Y.)
| | - Yujuan Yu
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.H.); (Y.Y.)
| | - Rober Kemperman
- Lesaffre Insituut of Science and Technology, 101 Rue de Menin, 59700 Marc-en-Baroeul, France; (R.K.); (L.J.)
| | - Luciana Jimenez
- Lesaffre Insituut of Science and Technology, 101 Rue de Menin, 59700 Marc-en-Baroeul, France; (R.K.); (L.J.)
| | - Faizan Ahmed Sadiq
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff CF14 4XY, UK;
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Burgemeester Van Gansberghelaan 92/1, 9820 Merelbeke, Belgium
| | - Guohua Zhang
- School of Life Science, Shanxi University, Taiyuan 030006, China; (X.H.); (Y.Y.)
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Ensiled Mixed Vegetables Enriched Carbohydrate Metabolism in Heterofermentative Lactic Acid Bacteria. FERMENTATION 2022. [DOI: 10.3390/fermentation8120699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
This study evaluated the fermentation quality, nutritive profile, in vitro fermentation, and microbial communities colonising sorghum ensiled with an unsalable vegetable mixture (chopped beans, carrot, and onion (1:1:1) ) including: (1)−100% sorghum; (2)−80% sorghum + 20% vegetable mix or (3)−60% sorghum + 40% vegetable mix, on a dry matter (DM) basis, with or without a probiotic inoculant. Samples were obtained across 0, 1, 3, 5,7, and 101 days ensiling and after 14 d aerobic exposure. The V4 region of the 16S rRNA gene and the ITS1 region were sequenced to profile bacterial, archaeal, and fungal communities. Compared to the 0% DM, ethanol increased (p < 0.01) from 8.42 to 20.4 ± 1.32 mM with 40% DM vegetable mix inclusion, while lactate decreased from 5.93 to 2.24 ± 0.26 mM. Linear discriminant analysis revealed that relative abundances of 12 bacterial taxa were influenced by silage treatments (log LDA score ≥ 4.02; p ≤ 0.03), while predicted functional pathways of alternative carbohydrate metabolism (hexitol, sulfoquinovose and glycerol degradation; N-acetyl glucosamine biosynthesis; log LDA score ≥ 2.04; p ≤ 0.02) were similarly enriched. This study indicated that carbohydrate metabolism by heterofermentative lactic acid bacteria can increase the feed value of sorghum when ensiled with an unsalable vegetable mixture at 40%DM, without requiring a high quantity of lactate.
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Boyaci Gunduz CP, Agirman B, Gaglio R, Franciosi E, Francesca N, Settanni L, Erten H. Evaluation of the variations in chemical and microbiological properties of the sourdoughs produced with selected lactic acid bacteria strains during fermentation. Food Chem X 2022; 14:100357. [PMID: 35693452 PMCID: PMC9178471 DOI: 10.1016/j.fochx.2022.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022] Open
Abstract
Chemical, microbiological and VOCs profile showed the relevance of starter addition. MiSeq Illumina confirmed that Lactobacillus spp. constituted the major LAB group. Fructilactobacillus sanfranciscensis was the most isolated LAB species. Rapid acidifying LAB strains should be preferred for sourdough production. Number of VOCs increased in sourdoughs produced with starter culture.
This research aimed to analyze variations in chemical properties, microbiological characteristics and generated volatile organic compounds (VOCs) profile during sourdough fermentation. Sourdoughs were collected from different cities in Turkey at two different times and lactic acid bacteria (LAB) in the samples were identified with culture-independent and culture-dependent molecular methods. According to culture-dependent methodology, thirteen LAB species were identified. Lactobacillus spp. were identified as the major group according to MiSeq Illumina analysis. Technological potential of commonly isolated LAB species was evaluated. Due to high frequency of isolation, Fructilactobacillus sanfranciscensis and Lactiplantibacillus plantarum strains were better investigated for their technological traits useful in sourdough production. Experimental sourdoughs were produced with mono- and dual-culture of the selected strains and chemical properties and microbiological characteristics, as well as VOCs profile of the sourdoughs, were subjected to multivariate analysis which showed the relevance of added starter, in terms of acidification and VOCs profile.
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Lin L, Du R, Wang Y, Wu Q, Xu Y. Regulation of auxotrophic lactobacilli growth by amino acid cross-feeding interaction. Int J Food Microbiol 2022; 377:109769. [DOI: 10.1016/j.ijfoodmicro.2022.109769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/04/2022] [Accepted: 05/29/2022] [Indexed: 12/09/2022]
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Mechanistic Insight into Yeast Bloom in a Lactic Acid Bacteria Relaying-Community in the Start of Sourdough Microbiota Evolution. Microbiol Spectr 2021; 9:e0066221. [PMID: 34668750 PMCID: PMC8528097 DOI: 10.1128/spectrum.00662-21] [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] [Indexed: 01/04/2023] Open
Abstract
The spontaneous microbiota of wheat sourdough, often comprising one yeast species and several lactic acid bacteria (LAB) species, evolves over repeated fermentation cycles, which bakers call backslopping. The final product quality largely depends on the microbiota functions, but these fluctuate sometimes during the initial months of fermentation cycles due to microbiota evolution in which three phases of LAB relay occur. In this study, the understanding of yeast-LAB interactions in the start of the evolution of the microbiota was deepened by exploring the timing and trigger interactions when sourdough yeast entered a preestablished LAB-relaying community. Monitoring of 32 cycles of evolution of 6 batches of spontaneous microbiota in wheat sourdoughs revealed that sourdough yeasts affected the LAB community when the 2nd- or 3rd-relaying types of LAB genera emerged. In in vitro pairwise cocultures, all 12 LAB strains containing the 3 LAB-relaying types arrested the growth of a Saccharomyces cerevisiae strain, a frequently found species in sourdoughs, to various extents by sugar-related interactions. These findings suggest competition due to different affinities of each LAB and a S. cerevisiae strain for each sugar. In particular, maltose was the driver of S. cerevisiae growth in all pairwise cocultures. The functional prediction of sugar metabolism in sourdough LAB communities showed a positive correlation between maltose degradation and the yeast population. Our results suggest that maltose-related interactions are key factors that enable yeasts to enter and then settle in the LAB-relaying community during the initial part of evolution of spontaneous sourdough microbiota. IMPORTANCE Unpredictable evolution of spontaneous sourdough microbiota sometimes prevents bakers from making special-quality products because the unstable microbiota causes the product quality to fluctuate. Elucidation of the evolutionary mechanisms of the sourdough community, comprising yeast and lactic acid bacteria (LAB), is fundamental to control fermentation performance. This study investigated the mechanisms by which sourdough yeasts entered and settled in a bacterial community in which a three-phase relay of LAB occurred. Our results showed that all three layers of LAB restricted the cohabiting yeast population by competing for the sugar sources, particularly maltose. During the initial evolution of spontaneous sourdough microbiota, yeasts tended to grow synchronously with the progression of the lactic acid bacterial relay, which was predictably associated with changes in the maltose degradation functions in the bacterial community. Further study of ≥3 species’ interactions while considering yeast diversity can uncover additional interaction mechanisms driving the initial evolution of sourdough microbiota.
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Yeasts and Lactic Acid Bacteria for Panettone Production: An Assessment of Candidate Strains. Microorganisms 2021; 9:microorganisms9051093. [PMID: 34069676 PMCID: PMC8160612 DOI: 10.3390/microorganisms9051093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022] Open
Abstract
The recovery of yeasts and lactic acid bacteria (LAB) involved in sourdough fermentation is the first step in the selection of starters with suitable technological aptitude and capable of producing desired aromas and/or aromatic precursors. In this work, two sourdoughs samples (MA and MB) and the derived doughs (samples A and B) were collected from a bakery during artisanal Panettone manufacture. Yeasts and bacteria were isolated at different fermentation steps on selective agar media. A total of 77 isolates were obtained and characterized. Representative strains of yeasts and LAB were identified by sequencing the D1/D2 domain of the 26S rRNA and the 16S rRNA genes, respectively. Moreover, the volatile organic compounds (VOCs) produced in the collected samples were detected and correlated to the species found in the same samples. The results highlighted the occurrence of Kazachstania humilis in both samples A and B, while Saccharomyces cerevisiae strains were detected only in samples B. Among LAB, Fructilactobacillus sanfranciscensis was the main species detected in both sourdoughs. Furthermore, strains belonging to the species Lactiplantibacillus plantarum, Furfurilactobacillus rossiae, Lactobacillus parabuchneri, Leuconostoc citreum, and Leuconostoc mesenteroides were assessed in the dough samples.
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