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Idowu AP, Yamamoto K, Koizumi T, Matsutani M, Takada K, Shiwa Y, Asfaw A, Matsumoto R, Ouyabe M, Pachakkil B, Kikuno H, Shiwachi H. Changes in the rhizosphere and root-associated bacteria community of white Guinea yam ( Dioscorea rotundata Poir.) impacted by genotype and nitrogen fertilization. Heliyon 2024; 10:e33169. [PMID: 39021943 PMCID: PMC11252748 DOI: 10.1016/j.heliyon.2024.e33169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
The bacterial diversity and composition of water yam (Dioscorea alata L. cv. A-19), which can grow without chemical fertilization, have recently been characterized with no significant differences compared with the use of chemical fertilization. However, the diversity and community structure of bacteria associated with the white Guinea yam (Dioscorea rotundata), the most cultivated and economically important yam in West Africa, have not yet been investigated. This study characterized the bacterial diversity and composition associated with bulk soil, rhizosphere, and plant roots in six white Guinea yam genotypes (S004, S020, S032, S042, S058, and S074) in field experiments in Ibadan, Nigeria under N-based chemical fertilizer application. The largest diversity of bacteria was found in the bulk soil, followed by the rhizosphere and roots. Based on the alpha diversity analysis, the bacterial diversity in both S020 and S042 increased with fertilizer application among the bulk soil samples. S058 grown under no-fertilizer conditions had the highest bacterial diversity among the rhizosphere samples. Beta diversity analysis highlighted the significant difference in the composition of bacteria associated with the genotypes and fertilizer treatments, and S032 had a unique bacterial composition compared to the other genotypes. The dominant phylum across all sample types was Proteobacteria. Actinobacteriota was the dominant phylum among bulk soil samples. At the genus level, Bacillus was the most abundant bacterial genus across both the control and treated samples. Pseudomonas was predominant across all rhizosphere samples. Chryseobacterium, Sphingobium, Delftia and Klebsiella associated with the rhizosphere were shown the altered relative abundance between the control and treated samples depending on genotypes. A genus related to symbiotic nitrogen-fixing bacteria, the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, showed higher relative abundance among all root samples, indicating that it is a core bacterial genus. Furthermore, the field application of chemical fertilizer had a significant impact on the relative abundances of two genera related to symbiotic nitrogen-fixers, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade and Bradyrhizobium in the rhizosphere and root. These results suggest that N-based chemical fertilizers and plant genotypes would influence the compositional arrangement of associated bacterial communities, including symbiotic nitrogen-fixing bacteria.
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Affiliation(s)
- Ayodeji Peter Idowu
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Takahiko Koizumi
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Kanako Takada
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), PMB 5320 Oyo Road Ibadan, Nigeria
| | - Ryo Matsumoto
- International Institute of Tropical Agriculture (IITA), PMB 5320 Oyo Road Ibadan, Nigeria
| | - Michel Ouyabe
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Babil Pachakkil
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Hidehiko Kikuno
- Miyako Subtropical Training and Research Farm, Tokyo University of Agriculture, Okinawa, Japan
| | - Hironobu Shiwachi
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
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Junker R, Valence F, Mistou MY, Chaillou S, Chiapello H. Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables. Microbiol Spectr 2024; 12:e0031224. [PMID: 38747598 PMCID: PMC11237590 DOI: 10.1128/spectrum.00312-24] [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: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024] Open
Abstract
The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the "stochastic block model" method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages. IMPORTANCE Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.
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Affiliation(s)
- Romane Junker
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
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Bai Y, Wu D, Dolfing J, Zhang L, Xie B. Dynamics and functions of biomarker taxa determine substrate-specific organic waste composting. BIORESOURCE TECHNOLOGY 2024; 393:130118. [PMID: 38029801 DOI: 10.1016/j.biortech.2023.130118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 12/01/2023]
Abstract
Bacteria are an influential component of diverse composting microbiomes, but their structure and underlying dynamics are poorly understood. This study analyzed the bacterial communities of 577 compost datasets globally and constructed a substrate-dependent catalog with more than 15 million non-redundant 16S rRNA gene sequences. Using a random-forest machine-learning model, 30 biomarker taxa were identified that accurately distinguish between the food, sludge and manure waste composting microbiomes (accuracy >98 %). These biomarker taxa were closely associated with carbon and nitrogen metabolic processes, during which they contributed to the predominant stochastic process and are influenced by different factors in the substrate-specific composts. This is corroborated by the community topological characteristics, which feature the biomarkers as keystone taxa maintaining the bacterial network stability. These findings provide a theoretical basis to identify and enhance the biomarker-functional bacteria for optimizing the composting performance of different organic wastes.
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Affiliation(s)
- Yudan Bai
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Jan Dolfing
- Faculty Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, United Kingdom
| | - Liangmao Zhang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Çelik Doğan C, Yüksel Dolgun HT, İkiz S, Kırkan Ş, Parın U. Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis. Foods 2023; 12:3538. [PMID: 37835192 PMCID: PMC10572611 DOI: 10.3390/foods12193538] [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: 08/23/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.
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Affiliation(s)
- Cansu Çelik Doğan
- Food Technology Program, Food Processing Department, Vocational School of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320 Istanbul, Türkiye
| | - Hafize Tuğba Yüksel Dolgun
- Department of Microbiology, Faculty of Veterinary Medicine, Aydın Adnan Menderes University, 09010 Aydın, Türkiye; (H.T.Y.D.); (Ş.K.); (U.P.)
| | - Serkan İkiz
- Department of Microbiology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320 Istanbul, Türkiye;
| | - Şükrü Kırkan
- Department of Microbiology, Faculty of Veterinary Medicine, Aydın Adnan Menderes University, 09010 Aydın, Türkiye; (H.T.Y.D.); (Ş.K.); (U.P.)
| | - Uğur Parın
- Department of Microbiology, Faculty of Veterinary Medicine, Aydın Adnan Menderes University, 09010 Aydın, Türkiye; (H.T.Y.D.); (Ş.K.); (U.P.)
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Kim SJ, Lee HW, Lee JY, Moon EW, Song H, Ha JH. Comparison of inactivation kinetics of Yersinia enterocolitica in vegan and non-vegan kimchi during fermentation. Heliyon 2023; 9:e15031. [PMID: 37095920 PMCID: PMC10121824 DOI: 10.1016/j.heliyon.2023.e15031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Yersinia enterocolitica is occasionally detected in kimchi, a traditional food prepared from fermented vegetables. Changes in growth properties of Y. enterocolitica during kimchi fermentation are largely unknown. We investigated the viability of Y. enterocolitica during the fermentation of vegan and non-vegan kimchi at different temperatures. Changes in Y. enterocolitica population, pH, and titratable acidity were measured for 24 days. In a suspension test with kimchi juice, populations of three Y. enterocolitica strains were above 3.30 log10 CFU/mL at pH > 5 for 7 days. Yersinia enterocolitica counts in vegan kimchi were considerably reduced at 0 °C and 6 °C. During fermentation at 6 °C, Y. enterocolitica populations in non-vegan kimchi and vegan kimchi were not detected starting from days 14 and 10, respectively. In kimchi samples stored at 0 °C and 6 °C, Y. enterocolitica survival correlated with pH changes during fermentation; in samples stored for up to 24 days, Y. enterocolitica was not detected. According to the k max values from the "log-linear with shoulder and tail" model, Y. enterocolitica was more sensitive to vegan kimchi fermentation than to non-vegan kimchi fermentation. Our findings provide an important basis for ensuring the safe production of kimchi without Y. enterocolitica contamination. Further research is necessary to elucidate the mechanism of Y. enterocolitica inactivation and the major bacterial and physicochemical factors involved in kimchi fermentation.
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Liswadiratanakul S, Yamamoto K, Matsutani M, Wattanadatsaree V, Kihara S, Shiwa Y, Shiwachi H. Replacement of water yam ( Dioscorea alata L.) indigenous root endophytes and rhizosphere bacterial communities via inoculation with a synthetic bacterial community of dominant nitrogen-fixing bacteria. Front Microbiol 2023; 14:1060239. [PMID: 36814567 PMCID: PMC9939703 DOI: 10.3389/fmicb.2023.1060239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/05/2023] [Indexed: 02/09/2023] Open
Abstract
Biofertilizers containing high-density plant growth-promoting bacteria are gaining interest as a sustainable solution to environmental problems caused by eutrophication. However, owing to the limitations of current investigative techniques, the selected microorganisms are not always preferred by the host plant, preventing recruitment into the native microbiota or failing to induce plant growth-promoting effects. To address this, five nitrogen-fixing bacteria previously isolated from water yam (Dioscorea alata L.) plants and showing dominant abundance of 1% or more in the water yam microbiota were selected for analysis of their plant growth-promoting activities when used as a synthetic bacterial inoculant. Water yam cv. A-19 plants were inoculated twice at 10 and 12 weeks after planting under greenhouse conditions. Bacterial communities in root, rhizosphere, and bulk soil samples were characterized using high-throughput 16S rRNA amplicon sequencing. Compared with non-inoculated plants, all bacterial communities were significantly altered by inoculation, mainly at the genus level. The inoculation effects were apparently found in the root communities at 16 weeks after planting, with all inoculated genera showing dominance (in the top 35 genera) compared with the control samples. However, no significant differences in any of the growth parameters or nitrogen contents were observed between treatments. At 20 weeks after planting, the dominance of Stenotrophomonas in the inoculated roots decreased, indicating a decline in the inoculation effects. Interestingly, only the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was dominant (>1% relative abundance) across all samples, suggesting that bacteria related to this clade are essential core bacteria for water yam growth. This is the first report on addition of a synthetic nitrogen-fixing bacterial community in water yam plants showing that native bacterial communities can be replaced by a synthetic bacterial community, with declining in the effects of Stenotrophomonas on the modified communities several weeks after inoculation.
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Affiliation(s)
- Sumetee Liswadiratanakul
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan,*Correspondence: Kosuke Yamamoto,
| | | | - Vatanee Wattanadatsaree
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Shunta Kihara
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan,NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Hironobu Shiwachi
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
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Xing S, Zhang X, Guan H, Li H, Liu W. Predictive model for growth of Leuconostoc mesenteroides in Chinese cabbage juices with different salinities. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Sørensen JS, Madsen SK, Bang-Berthelsen CH, Hansen LT. Quality and safety aspects in fermentation of winged kelp (Alaria esculenta) and sugar kelp (Saccharina latissima) by the natural microbiota with or without addition of a Lactiplantibacillus plantarum starter culture. Food Res Int 2021; 150:110800. [PMID: 34863492 DOI: 10.1016/j.foodres.2021.110800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/22/2021] [Accepted: 11/01/2021] [Indexed: 01/04/2023]
Abstract
Nourishment of the growing human population requires new and alternative food sources, preferable produced without occupying new land areas. Cultivation of seaweed presents an opportunity, however, a major obstacle is sustainable preservation. Fermentation has been used for centuries to preserve vegetables, e.g., to produce kimchi based on cabbage. This study investigated changes in the microbiota, characteristics (pH, organic acids and water soluble carbohydrates) and food safety of raw shredded Alaria esculenta and Saccharina latissima during fermentation by the natural microbiota with or without addition of a Lactiplantibacillus plantarum starter culture. The Lb. plantarum fermented products retained a high Shannon diversity index, indicating a partially unsuccessful fermentation. Lb. plantarum performed better in A. esculenta causing pH to drop to below 4.6, a critical limit for control of growth of Clostridium botulinum, within 2 days compared to 7 days for S. latissima. Natural fermentation by the endogenous microbiota resulted in unsafe products with high final pH values (4.8-5.2), presence of unwanted organic acids, such as butyric acid, and in the case of A. esculenta sustenance of inoculated Listeria monocytogenes. Fermentation of A. esculenta and S. latissima by Lb. plantarum is a promising preservation method. However, future work is needed to optimise the process, by investigation of the use of different starter cultures, seaweed pre-treatments (blanching, freezing, etc.) and adjuvants (i.e., addition of sugars, minerals and similar) to promote growth of the starter culture and ensure the fermented products are safe to eat.
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Affiliation(s)
| | - Sanne Kjærulf Madsen
- The National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Lee JH, Choi EJ, Chang JY, Song KB, Chun HH. Effect of high hydrostatic pressure (HHP) and supercooling storage in leaf mustard (Brassica juncea L.) kimchi: Modelling of microbial activity and preservation of physicochemical properties. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Yamamoto K, Matsutani M, Shiwa Y, Ishige T, Sakamoto H, Saitoh H, Tsushima S. Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan. Microbes Environ 2021; 35. [PMID: 32893195 PMCID: PMC7511784 DOI: 10.1264/jsme2.me20072] [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] [Indexed: 01/04/2023] Open
Abstract
Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.
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Affiliation(s)
- Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | | | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture.,NODAI Genome Research Center, Tokyo University of Agriculture
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of Agriculture
| | - Hikaru Sakamoto
- Department of Northern Biosphere Agriculture, Faculty of Bioindustry, Tokyo University of Agriculture
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Seiya Tsushima
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
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Lee HJ, Lee MJ, Choi YJ, Park SJ, Lee MA, Min SG, Park SH, Seo HY, Yun YR. Free Amino Acid and Volatile Compound Profiles of Jeotgal Alternatives and Its Application to Kimchi. Foods 2021; 10:foods10020423. [PMID: 33671949 PMCID: PMC7919035 DOI: 10.3390/foods10020423] [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: 01/11/2021] [Revised: 02/06/2021] [Accepted: 02/12/2021] [Indexed: 11/16/2022] Open
Abstract
Jeotgal containing abundant free amino acids plays an important role in the unique savory taste (umami) and flavor in kimchi. However, it is also responsible for the unpleasant fishy smell and high salt content of kimchi. Therefore, the present study aimed to identify alternative jeotgal sources and investigate the fermentation properties of jeotgal alternatives added to kimchi. The tomato hot-water extract (TH2) and dry-aged beef hot-water extract (DBH) were selected as jeotgal alternatives for kimchi preparation based on their glutamic acid contents. Characteristics of kimchi with TH2 alone (JA1) and TH2 and DBH in combination (1:1, JA2) were compared with kimchi prepared using commercially available anchovy fish sauce (CON). The pH of JA1 and JA2 was slightly decreased during fermentation, whereas the salinity was significantly lower than CON (p < 0.05). Notably, the most effective factor of the savory taste of kimchi, glutamic acid contents of JA1 and JA2 were significantly higher than that of CON (p < 0.05). In conclusion, JA1 showed slower fermentation with lower salinity and higher glutamic acid content than CON. Overall, this study showed that JA1 derived from TH2 could improve the taste and quality of kimchi by increasing glutamic acid content and decreasing the unpleasant flavor.
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Affiliation(s)
- Hye Jin Lee
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Min Jung Lee
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Yun-Jeong Choi
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Sung Jin Park
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Mi-Ai Lee
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Sung Gi Min
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Sung-Hee Park
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
| | - Hye-Young Seo
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, Korea;
| | - Ye-Rang Yun
- Industrial Technology Research Group, World Institute of Kimchi, Gwangju 61755, Korea; (H.J.L.); (M.J.L.); (Y.-J.C.); (S.J.P.); (M.-A.L.); (S.G.M.); (S.-H.P.)
- Correspondence: ; Tel.: +82-626-101-849; Fax: +82-626-101-850
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Endo A, Koizumi R, Nakazawa Y, Shiwa Y, Maeno S, Kido Y, Irisawa T, Muramatsu Y, Tada K, Yamazaki M, Myoda T. Characterization of the microbiota and chemical properties of pork loins during dry aging. Microbiologyopen 2021; 10:e1157. [PMID: 33415844 PMCID: PMC7914123 DOI: 10.1002/mbo3.1157] [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: 08/17/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Dry aging (DA) allows for the storage of meat without packaging at 0 to 3°C for several weeks. It enhances the production of pleasant flavors, tenderness, and juiciness in meat. Due to the long storage period and roles of indigenous microbiota in the maturation of several meat products, the microbiota of DA meat is of interest in terms of microbial contributions and food hygiene but has not yet been characterized in detail. This study identified the microbiota of pork loins during DA using culturing and culture‐independent meta‐16S rRNA gene sequencing and elucidated its characteristics. The amounts of free amino acids and profiles of aroma‐active compounds were also monitored by high‐performance liquid chromatography and gas chromatography, respectively. The meta‐16S rRNA gene sequencing revealed that Pseudomonas spp. generally dominated the microbiota throughout DA; however, the culturing analysis showed marked changes in the species composition during DA. Acinetobacter spp. were the second most dominant bacteria before DA in the culture‐independent analysis but became a minor population during DA. The cell numbers of yeasts showed an increased tendency during DA, and Debaryomyces hansenii was the only microorganism isolated from all meat samples throughout DA. Well‐known foodborne pathogens were not observed in two microbiota analyses. The amounts of free amino acids were increased by DA, and the number of aroma‐active compounds and their flavor dilution values markedly changed during DA. Most microbial isolates showed positive reactions with proteolytic and lipolytic activities, suggesting their contribution to tenderness and aroma production in DA meats.
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Affiliation(s)
- Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Ryosuke Koizumi
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan.,Department of Agricultural Innovation for Sustainability, Faculty of Agriculture, Tokyo University of Agriculture, Kanagawa, Japan
| | - Yozo Nakazawa
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Yoshihiko Kido
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Tomohiro Irisawa
- Department of Agricultural Innovation for Sustainability, Faculty of Agriculture, Tokyo University of Agriculture, Kanagawa, Japan
| | - Yoshiki Muramatsu
- Department of Bioproduction and Environment Engineering, Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Kotaro Tada
- Department of Agricultural Innovation for Sustainability, Faculty of Agriculture, Tokyo University of Agriculture, Kanagawa, Japan
| | - Masao Yamazaki
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Takao Myoda
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
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13
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Probiotic characteristics of Lactobacillus brevis B13-2 isolated from kimchi and investigation of antioxidant and immune-modulating abilities of its heat-killed cells. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109452] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Sui HY, Weil AA, Nuwagira E, Qadri F, Ryan ET, Mezzari MP, Phipatanakul W, Lai PS. Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing. Front Microbiol 2020; 11:953. [PMID: 32528434 PMCID: PMC7262970 DOI: 10.3389/fmicb.2020.00953] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/21/2020] [Indexed: 12/26/2022] Open
Abstract
Both the host microbiome and the microbiome of the built environment can have profound impacts on human health. While prior studies have suggested that the variability introduced by DNA extraction method is less than typical biologic variation, most studies have focused on 16S rRNA amplicon sequencing or on high biomass fecal samples. Shotgun metagenomic sequencing provides advantages over amplicon sequencing for surveying the microbiome, but is a challenge to perform in lower microbial biomass samples with high human DNA content such as sputum or vacuumed dust. Here we systematically evaluate the impact of four different extraction methods (phenol:choloroform, and three high-throughput kit-based approaches, the Promega Maxwell gDNA, Qiagen MagAttract PowerSoil DNA, and ZymoBIOMICS 96 MagBead). We report the variation in microbial community structure and predicted microbial function assessed by shotgun metagenomics sequencing in human stool, sputum, and vacuumed dust obtained from ongoing cohort studies or clinical trials. The same beadbeating protocol was used for all samples to focus our evaluation on the impact of kit chemistries on sequencing results. DNA yield was overall highest in the phenol:choloroform and Promega approaches. Only the phenol:choloroform approach showed evidence of contamination in negative controls. Bias was evaluated using mock community controls, and was noted across all extraction methods, although Promega exhibited the least amount of bias. The extraction method did not impact the proportion of human reads, although stool had the lowest proportion of human reads (0.1%) as compared to dust (44.1%) and sputum (80%). We calculated Bray-Curtis dissimilarity and Aitchison distances to evaluate the impact of extraction method on microbial community structure by sample type. Extraction method had the lowest impact in stool (extraction method responsible for 3.0-3.9% of the variability), the most impact in vacuumed dust (12-16% of the variability) and intermediate values for sputum (9.2-12% variability). Similar differences were noted when evaluating microbial community function. Our results will inform investigators planning microbiome studies using diverse sample types in large clinical studies. A consistent DNA extraction approach across all sample types is recommended, particularly with lower microbial biomass samples that are more heavily influenced by extraction method.
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Affiliation(s)
- Hui-yu Sui
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Ana A. Weil
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Edwin Nuwagira
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Melissa P. Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Wanda Phipatanakul
- Harvard Medical School, Boston, MA, United States
- Division of Immunology, Boston Children’s Hospital, Boston, MA, United States
| | - Peggy S. Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Immunology, Boston Children’s Hospital, Boston, MA, United States
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15
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Zhang L, Zhang Y, Patterson J, Arslan M, Zhang Y, Gamal El-Din M. Biofiltration of oil sands process water in fixed-bed biofilm reactors shapes microbial community structure for enhanced degradation of naphthenic acids. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137028. [PMID: 32109809 DOI: 10.1016/j.scitotenv.2020.137028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/12/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Naphthenic acids (NAs) are a complex mixture of carboxylic acids present in oil sands process water (OSPW). Their recalcitrant nature makes them difficult to be removed from the environment using conventional remediation strategies. This study hypothesized that, upon continuous operation, biofiltration of OSPW in fixed-bed biofilm reactors would allow the development of NA-degrading microbial community within the biofilter following successful removal. Both raw and ozonated OSPW were treated in the biofilters and changes in microbial community were tested via 16S/18S amplicon sequencing and metatranscriptomics. Through switch from suspended growth to attached growth, a shift in indigenous microbial community was seen following by an increase in alpha diversity. Concomitantly, improved degradation of NAs was monitored, i.e., 35.8% and 69.4% of NAs were removed from raw and ozonated OSPW, respectively. Metatranscriptomics analysis suggested the presence of genes involved in the degradation of organic acids and petroleum-related compounds. Specifically, functional abundance of aromatic compounds' metabolism improved from 0.05% to 0.76%; whereas abundance of benzoate transport and degradation pathway increased from 0.04% to 0.64%. These changes conclude that continuous operation of OSPW in the bioreactors was in favor of shaping the overall microbiome towards better NA degradation.
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Affiliation(s)
- Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada; Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, PR China
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM 88003, United States
| | - Jordan Patterson
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, PR China
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada.
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16
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Lee M, Song JH, Park JM, Chang JY. Bacterial diversity in Korean temple kimchi fermentation. Food Res Int 2019; 126:108592. [DOI: 10.1016/j.foodres.2019.108592] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 01/02/2023]
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17
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Combined effects of high hydrostatic pressure treatment and red ginseng concentrate supplementation on the inactivation of foodborne pathogens and the quality of ready-to-use kimchi sauce. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Hwang IM, Yang JS, Jung JH, Lee HW, Lee HM, Seo HY, Khan N, Jamila N, Kim KS, Kim SH. Dietary intake assessment of macro, trace, and toxic elements via consumption of kimchi in South Korea. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:6474-6481. [PMID: 31294829 DOI: 10.1002/jsfa.9926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/28/2019] [Accepted: 07/08/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Kimchi, a Korean food, is now produced and consumed in many other countries. In this study, the macro, trace, and toxic element content in varieties of kimchi from Korea and China was evaluated. A health-risk assessment, involving the calculation of estimated dietary intake values, was undertaken. To discriminate among samples with different origins, linear discriminant analysis (LDA) and principal component analysis (PCA) were applied. RESULTS The analytical methods used for analyses were successfully validated. In the quantification of elements, no significant differences were detected in the concentrations of the elements that were analyzed. Based on the fresh weight of kimchi, among the macro elements, the concentrations of Na and K were relatively high, with values of 4181.9-9919.8 mg kg-1 and 1661.8-6623.5 mg kg-1 , respectively. Among the trace elements that were analyzed, zinc in Korean samples, and strontium in Chinese samples showed the highest concentrations, at 2.67 and 2.98 mg kg-1 , respectively. Concentration levels of the toxic trace elements were within permissible limits. The amount of daily intake and provisional daily intake of each element calculated based on kimchi intake confirmed its safety for consumption. Linear discriminant analysis and PCA successfully discriminated among the samples of Chinese and Korean origin. CONCLUSION The provisional daily intake of the toxic elements was within provisional tolerable daily intake values. The normal intake of kimchi could not pose a threat upon consumption. © 2019 Society of Chemical Industry.
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Affiliation(s)
- In Min Hwang
- World Institute of Kimchi, Gwangju, Republic of Korea
| | - Ji-Su Yang
- World Institute of Kimchi, Gwangju, Republic of Korea
| | - Ji-Hye Jung
- World Institute of Kimchi, Gwangju, Republic of Korea
| | - Hae-Won Lee
- World Institute of Kimchi, Gwangju, Republic of Korea
| | - Hee Min Lee
- World Institute of Kimchi, Gwangju, Republic of Korea
| | - Hye-Young Seo
- World Institute of Kimchi, Gwangju, Republic of Korea
| | - Naeem Khan
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Nargis Jamila
- Department of Chemistry, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Kyong Su Kim
- Department of Food and Nutrition, Chosun University, Gwangju, Republic of Korea
| | - Sung Hyun Kim
- World Institute of Kimchi, Gwangju, Republic of Korea
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19
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Establishment Limitation Constrains the Abundance of Lactic Acid Bacteria in the Napa Cabbage Phyllosphere. Appl Environ Microbiol 2019; 85:AEM.00269-19. [PMID: 31003989 DOI: 10.1128/aem.00269-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022] Open
Abstract
Patterns of phyllosphere diversity have become increasingly clear with high-throughput sequencing surveys, but the processes that control phyllosphere diversity are still emerging. Through a combination of lab and field experiments using Napa cabbage and lactic acid bacteria (LAB), we examined how dispersal and establishment processes shape the ecological distributions of phyllosphere bacteria. We first determined the abundance and diversity of LAB on Napa cabbage grown at three sites using both culture-based approaches and 16S rRNA gene amplicon sequencing. Across all sites, LAB made up less than 0.9% of the total bacterial community abundance. To assess whether LAB were low in abundance in the Napa cabbage phyllosphere due to a limited abundance in local species pools (source limitation), we quantified LAB in leaf and soil samples across 51 vegetable farms and gardens throughout the northeastern United States. Across all sites, LAB comprised less than 3.2% of the soil bacterial communities and less than 1.6% of phyllosphere bacterial communities. To assess whether LAB are unable to grow in the phyllosphere even if they dispersed at high rates (establishment limitation), we used a gnotobiotic Napa cabbage system in the lab with experimental communities mimicking various dispersal rates of LAB. Even at high dispersal rates, LAB became rare or completely undetectable in experimental communities, suggesting that they are also establishment limited. Collectively, our data demonstrate that the low abundance of LAB in phyllosphere communities may be explained by establishment limitation.IMPORTANCE The quality and safety of vegetable fermentations are dependent on the activities of LAB naturally present in the phyllosphere. Despite their critical role in determining the success of fermentation, the processes that determine the abundance and diversity of LAB in vegetables used for fermentation are poorly characterized. Our work demonstrates that the limited ability of LAB to grow in the cabbage phyllosphere environment may constrain their abundance on cabbage leaves. These results suggest that commercial fermentation of Napa cabbage proceeds despite low and variable abundances of LAB across different growing regions. Propagule limitation may also explain ecological distributions of other rare members of phyllosphere microbes.
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20
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Jeong D, Lee JH, Chung HJ. Analysis of Targeted Metabolites and Molecular Structure of Starch to Understand the Effect of Glutinous Rice Paste on Kimchi Fermentation. Molecules 2018; 23:molecules23123324. [PMID: 30558194 PMCID: PMC6320964 DOI: 10.3390/molecules23123324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/13/2018] [Accepted: 12/13/2018] [Indexed: 11/23/2022] Open
Abstract
Bachu (Chinese cabbage) kimchi, a Korean traditional fermented dish, were prepared with or without the addition of glutinous (waxy) rice paste and their characteristics including pH, total bacteria count, total starch content, sugar metabolites, and molecular structure of starch were examined periodically for 20 days to investigate the effect of adding glutinous rice paste to kimchi during fermentation. The pH and total bacteria count showed that the fermentation of kimchi added with glutinous rice paste (GRP kimchi) progressed a little more quickly than that of control kimchi without glutinous rice paste. The GRP kimchi had higher glucose content but lower fructose content than control kimchi. Interestingly, maltose was only detected in GRP kimchi during fermentation. The GRP kimchi contained much greater amount of mannitol throughout fermentation than control kimchi. Total starch content in GRP kimchi gradually decreased during fermentation, which might have contributed to its greater glucose content and the larger amount of maltose production. In GRP kimchi, peak height and area for all degrees of polymerization (DP) of starch decreased during fermentation and its average chain length decreased while the proportion of short chains increased as fermentation processed, indicating degradation of starch chains by enzymes presented in the kimchi.
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Affiliation(s)
- Duyun Jeong
- Division of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea.
| | - Jong-Hee Lee
- Research and Development Division, Advanced Process Technology and Fermentation Research Group, World Institute of Kimchi, Gwangju 61755, Korea.
| | - Hyun-Jung Chung
- Division of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea.
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21
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Yamamoto K, Shiwa Y, Ishige T, Sakamoto H, Tanaka K, Uchino M, Tanaka N, Oguri S, Saitoh H, Tsushima S. Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea. Front Microbiol 2018; 9:2878. [PMID: 30555434 PMCID: PMC6282094 DOI: 10.3389/fmicb.2018.02878] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.
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Affiliation(s)
- Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Hikaru Sakamoto
- Department of Northern Biosphere Agriculture, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Masataka Uchino
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Suguru Oguri
- Department of Northern Biosphere Agriculture, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Seiya Tsushima
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
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22
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Zabat MA, Sano WH, Wurster JI, Cabral DJ, Belenky P. Microbial Community Analysis of Sauerkraut Fermentation Reveals a Stable and Rapidly Established Community. Foods 2018; 7:E77. [PMID: 29757214 PMCID: PMC5977097 DOI: 10.3390/foods7050077] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 11/25/2022] Open
Abstract
Despite recent interest in microbial communities of fermented foods, there has been little inquiry into the bacterial community dynamics of sauerkraut, one of the world’s oldest and most prevalent fermented foods. In this study, we utilize 16S rRNA amplicon sequencing to profile the microbial community of naturally fermented sauerkraut throughout the fermentation process while also analyzing the bacterial communities of the starting ingredients and the production environment. Our results indicate that the sauerkraut microbiome is rapidly established after fermentation begins and that the community is stable through fermentation and packaging for commercial sale. Our high-throughput analysis is in agreement with previous studies that utilized traditional microbiological assessments but expands the identified taxonomy. Additionally, we find that the microbial communities of the starting ingredients and the production facility environment exhibit low relative abundance of the lactic acid bacteria that dominate fermented sauerkraut.
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Affiliation(s)
- Michelle A Zabat
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA.
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA.
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA.
| | - Damien J Cabral
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA.
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA.
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