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Balasubramanian R, Schneider E, Gunnigle E, Cotter PD, Cryan JF. Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health. Neurosci Biobehav Rev 2024; 158:105562. [PMID: 38278378 DOI: 10.1016/j.neubiorev.2024.105562] [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: 10/26/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 01/28/2024]
Abstract
Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though the microbiota-gut-brain axis. Fermented foods offer themselves as a combined whole food microbiota modulating intervention. Indeed, they contain potentially beneficial microbes, microbial metabolites and other bioactives, which are being harnessed to target the microbiota-gut-brain axis for positive benefits. This review highlights the diverse nature of fermented foods in terms of the raw materials used and type of fermentation employed, and summarises their potential to shape composition of the gut microbiota, the gut to brain communication pathways including the immune system and, ultimately, modulate the microbiota-gut-brain axis. Throughout, we identify knowledge gaps and challenges faced in designing human studies for investigating the mental health-promoting potential of individual fermented foods or components thereof. Importantly, we also suggest solutions that can advance understanding of the therapeutic merit of fermented foods to modulate the microbiota-gut-brain axis.
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Affiliation(s)
- Ramya Balasubramanian
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, P61C996, County Cork, Ireland
| | | | - Eoin Gunnigle
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, P61C996, County Cork, Ireland.
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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Elcheninov AG, Zayulina KS, Klyukina AA, Kremneva MK, Kublanov IV, Kochetkova TV. Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Microorganisms 2023; 12:16. [PMID: 38276185 PMCID: PMC10819033 DOI: 10.3390/microorganisms12010016] [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: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.
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Affiliation(s)
- Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Mariia K. Kremneva
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia;
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
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Wu S, Yang X, Gao H, Shi C, Wang L, Lu D, Li Y, Zhang J, Zhang W, Wen P. Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing. PeerJ 2023; 11:e14733. [PMID: 36718443 PMCID: PMC9884033 DOI: 10.7717/peerj.14733] [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: 09/22/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023] Open
Abstract
Background The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated. Methods In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function. Results After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.
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Affiliation(s)
- Shifang Wu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaoli Yang
- Gansu Institute of Business and Technology, Lanzhou, Gansu, China
| | - Haina Gao
- School of Food and Health, Beijing Technology & Business University, Beijing, Beijing, China
| | - Chengrui Shi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Longlin Wang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Deyuan Lu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yiheng Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jinliang Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Weibing Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Pengcheng Wen
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
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Alraddadi FA, Ross T, Powell SM. Evaluation of the microbial communities in kefir grains and kefir over time. Int Dairy J 2023. [DOI: 10.1016/j.idairyj.2022.105490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Environmental factors drive microbial succession and huangjiu flavor formation during raw wheat qu fermentation. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Bao W, He Y, Yu J, Yang X, Liu M, Ji R. Diversity analysis and gene function prediction of bacteria and fungi of Bactrian camel milk and naturally fermented camel milk from Alxa in Inner Mongolia. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kochetkova TV, Grabarnik IP, Klyukina AA, Zayulina KS, Elizarov IM, Shestakova OO, Gavirova LA, Malysheva AD, Shcherbakova PA, Barkhutova DD, Karnachuk OV, Shestakov AI, Elcheninov AG, Kublanov IV. Microbial Communities of Artisanal Fermented Milk Products from Russia. Microorganisms 2022; 10:microorganisms10112140. [PMID: 36363732 PMCID: PMC9697859 DOI: 10.3390/microorganisms10112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia. The examined FMPs were produced from cow, camel, mare’s or mixed milk, in the traditional way, without adding commercial starter cultures. Lactate and acetate were the major volatile fatty acids (VFA) of the studied FMPs, while succinate, formate, propionate and n-butyrate were present in lower concentrations. Bacterial communities analyzed by 16S rRNA gene V4 fragment amplicon sequencing showed that Firmicutes (Lactococcus, Lactobacillus, Streptococcus, Lentilactobacillus and Leuconostoc) was the predominant phylum in all analyzed FMPs, followed by Proteobacteria (Acetobacter, Klebsiella, Pseudomonas and Citrobacter). Lactobacillus (mainly in beverages) or Lactococcus (mainly in creamy and solid products) were the most abundant community-forming genera in FMPs where raw milk was used and fermentation took place at (or below) room temperature. In turn, representatives of Streptococcus genus dominated the FMPs made from melted or pasteurized milk and fermented at elevated temperatures (such as ryazhenka, cottage cheese and matsoni-like products). It was revealed that the microbial diversity of koumiss, shubat, ryazhenka, matsoni-like products, chegen, sour cream and bryndza varied slightly within each type and correlated well with the same products from other regions and countries. On the other hand, the microbiomes of kefir, prostokvasha, ayran, cottage cheese and suluguni-like cheese were more variable and were shaped by the influence of particular factors linked with regional differences and traditions expressed in specificities in the production process. The microbial diversity of aarts, khurunga, khuruud, tan, ayran and suluguni-like cheese was studied here, to our knowledge, for the first time. The results of this study emphasize the overall similarity of the microbial communities of various FMPs on the one hand, and specificities of regional products on the other. The latter are of particular value in the age of globalization when people have begun searching for new and unusual products and properties. Speaking more specifically, these novel products, with their characteristic communities, might be used for the development of novel microbial associations (i.e., starters) to produce novel products with improved or unique properties.
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Affiliation(s)
- Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
- Correspondence:
| | - Ilya P. Grabarnik
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 197101 Saint Petersburg, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | | | - Liliya A. Gavirova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | | | - Darima D. Barkhutova
- Institute of General and Experimental Biology Siberian Branch of the Russian Academy of Sciences, 600047 Ulan-Ude, Russia
| | - Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Andrey I. Shestakov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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Rahmeh R, Akbar A, Alomirah H, Kishk M, Al-Ateeqi A, Al-Milhm S, Shajan A, Akbar B, Al-Merri S, Alotaibi M, Esposito A. Camel milk microbiota: A culture-independent assessment. Food Res Int 2022; 159:111629. [DOI: 10.1016/j.foodres.2022.111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
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9
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Ren H, Deng Y, Wang X. Effect of a compound starter cultures inoculation on bacterial profile and biogenic amine accumulation in Chinese Sichuan sausages. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Characterization of the microbial community compositions and diversities in the traditional fermented yak milk from different ecotopes on the Qinghai-Tibetan plateau. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.113027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Demirci T, Akın N, Öztürk Hİ, Oğul A. A metagenomic approach to homemade back-slopped yogurts produced in mountainous villages of Turkey with the potential next-generation probiotics. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Sun Y, Yang J, Sun T, Liu W. Evaluation of lactic acid bacterial communities in spontaneously-fermented dairy products from Tajikistan, Kyrgyzstan and Uzbekistan using culture-dependent and culture-independent methods. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Liang T, Xie X, Zhang J, Ding Y, Wu Q. Bacterial community and composition of different traditional fermented dairy products in China, South Africa, and Sri Lanka by high-throughput sequencing of 16S rRNA genes. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111209] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Cao H, Yan Y, Wang L, Dong L, Pang X, Tang S, Li A, Xiang A, Zhang L, Zheng B. High-Throughput Sequencing Reveals Bacterial Diversity in Raw Milk Production Environment and Production Chain in Tangshan City of China. Food Sci Anim Resour 2021; 41:452-467. [PMID: 34017954 PMCID: PMC8112312 DOI: 10.5851/kosfa.2021.e10] [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: 11/17/2020] [Revised: 02/27/2021] [Accepted: 03/05/2021] [Indexed: 12/26/2022] Open
Abstract
Raw milk is a nature media of microbiota that access milk from various sources,
which constitutes a challenge in dairy production. This study characterizes the
relationship between the raw milk quality and the bacteria diversity at
different sampling sites in dairy farms, aiming to provide a strong scientific
basis for good hygienic practices and optimized procedure in milk production.
High-throughput sequencing of 16S rRNA V3-V4 region was used to analyze the
components, abundance and diversity of 48 bacterial population sampled from 8
different sites in dairy farm: pre-sterilized cow’s teats (C1),
post-sterilized cow’s teats (C2), milking cluster (E), milk in storage
tank (M1), transport vehicle (M2), storage equipment (E2), cow’s dung
samples (F) and drinking water (W). Firmicutes account for predominantly
32.36% (C1), 44.62% (C2), 44.71% (E), 41.10% (M1),
45.08% (M2), 53.38% (F) of all annotated phyla. Proteobacteria
accounts for 81.79% in W group and Actinobacteria 56.43% in E2
group. At the genus level, Acinetobacter was the most abundant
genus that causes bovine mastitis, Acinetobacter and
Arthrobacter were dominant in C1, C2, and E groups,
Kocuria in E2 group and Arcobacter in W group. E, C1, and
C2 group have very similar bacterial composition, and M1 and M2 demonstrated
similar composition, indicating that the milking cluster was polluted by the
environment or contact with cow udders. Bacterial population composition in
different sampling sites identified by NGS reveals a correlation between the
bacteria communities of raw milk production chain and the quality of raw
milk.
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Affiliation(s)
- Huihui Cao
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Yanhua Yan
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Lei Wang
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China
| | - Lixue Dong
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Xueliang Pang
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Sining Tang
- Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Aijun Li
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China
| | - Aili Xiang
- Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Litian Zhang
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
| | - Baiqin Zheng
- Tangshan Food and Drug Comprehensive Testing Center, Tangshan 063000, China.,Hebei Agricultural Products Quality and Safety Testing Innovation Center, Tangshan 063000, China.,Tangshan Institute of Industrial Technology for Functional Agricultural Products, Tangshan 063000, China
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Xu W, Li C, Guo Y, Zhang Y, Ya M, Guo L. A snapshot study of the microbial community dynamics in naturally fermented cow's milk. Food Sci Nutr 2021; 9:2053-2065. [PMID: 33841823 PMCID: PMC8020932 DOI: 10.1002/fsn3.2174] [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: 09/27/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 11/11/2022] Open
Abstract
Natural fermentation of milk is a prerequisite in the production of traditional dairy products and is considered a bioresource of fermentative microorganisms and probiotics. To understand the microbial dynamics during distinct fermentative phases, the roles of different microbes, and the relationship between bacteria and fungi, microbial community dynamics was investigated by culture-dependent and culture-independent approaches. Natural, static fermentation of milk induces the formation of the underlying curds and the superficial sour cream (Zuohe in the Mongolian language). From an overall perspective, viable LAB increased remarkably. Yeast showed an initial increase in their abundance (from 0 hr to 24 hr), which was followed by a decrease, and mold was detected at the later stages of fermentation (after 68 hr). The observed trends in microbiota variation suggest an antagonistic interaction between bacteria (LAB) and fungi (yeast and mold). The beneficial bacterial and fungal genus and species (e.g., Lactococcus, Streptococcus, Leuconostoc, Dipodascus, Lactococcus lacti, Dipodascus australiensis) are gradually increased in concentration, and the potentially detrimental microbial genus and species (e.g., Acinetobacter, Pseudomonas, Fusarium, Aspergillus, Mortierella, Acinetobacter johnsonii, Fusarium solani) decrease during the decline of bacterial and fungi diversity from natural fermentation. The study of microbial community dynamics could make a great contribution to understand the mechanism of natural fermentation of milk and the formation of curds and Zuohe, and to discover the potentially fermentative microbes for industrial starter cultures.
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Affiliation(s)
- Wei‐Liang Xu
- Xilingol Vocational CollegeXilin Gol Institute of BioengineeringXilin Gol Food Testing and Risk Assessment CenterXilinhotChina
| | - Chun‐Dong Li
- Xilingol Vocational CollegeXilin Gol Institute of BioengineeringXilin Gol Food Testing and Risk Assessment CenterXilinhotChina
| | - Yuan‐Sheng Guo
- Xilingol Vocational CollegeXilin Gol Institute of BioengineeringXilin Gol Food Testing and Risk Assessment CenterXilinhotChina
| | - Yi Zhang
- Xilingol Vocational CollegeXilin Gol Institute of BioengineeringXilin Gol Food Testing and Risk Assessment CenterXilinhotChina
| | - Mei Ya
- Xilingol Vocational CollegeXilin Gol Institute of BioengineeringXilin Gol Food Testing and Risk Assessment CenterXilinhotChina
| | - Liang Guo
- Xilingol Vocational CollegeXilin Gol Institute of BioengineeringXilin Gol Food Testing and Risk Assessment CenterXilinhotChina
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16
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El-Hajjaji S, Gérard A, De Laubier J, Lainé A, Patz V, Sindic M. Study of the bacterial profile of raw milk butter, made during a challenge test with Listeria monocytogenes, depending on cream maturation temperature. Food Microbiol 2021; 98:103778. [PMID: 33875207 DOI: 10.1016/j.fm.2021.103778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
Bacteria can play different roles and impart various flavors and characteristics to food. Few studies have described bacterial microbiota of butter. In this study, next-generation sequencing was used to determine bacterial content of raw milk butter, processed during a challenge test, depending on cream maturation temperature and on the presence or not of L. monocytogenes. Two batches were produced. pH and microbiological analyses were conducted during cream maturation and butter storage. DNA was also isolated from all samples for 16S rRNA amplicon sequencing analysis. For butter made from cream matured at 14 °C, a growth potential of L. monocytogenes of - 1.72 log cfu/g was obtained. This value corresponds to the difference between the median of counts at the end of storage and the median of counts at the beginning of storage. This butter (pH value of 4.75 ± 0.04) was characterized by a dominance of Lactococcus. The abundance of Lactococcus was significantly higher in inoculated samples than in control samples (p value < 0.05). Butter made from cream matured at 4 °C (pH value of 6.81 ± 0.01) presented a growth potential of 1.81 log cfu/g. It was characterized by the abundance of psychrotrophic bacteria mainly Pseudomonas. This study demonstrated that cream maturation temperature impacts butter microbiota, affecting thus product's characteristics and its ability to support or not the growth of pathogens like L. monocytogenes.
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Affiliation(s)
- Soundous El-Hajjaji
- Laboratory of Quality and Safety of Agro-food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium.
| | - Amaury Gérard
- Laboratory of Quality and Safety of Agro-food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Juliette De Laubier
- Laboratory of Quality and Safety of Agro-food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Aurélie Lainé
- Laboratory of Quality and Safety of Agro-food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Viviane Patz
- Laboratory of Quality and Safety of Agro-food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Marianne Sindic
- Laboratory of Quality and Safety of Agro-food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
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Peng C, Sun Z, Sun Y, Ma T, Li W, Zhang H. Characterization and association of bacterial communities and nonvolatile components in spontaneously fermented cow milk at different geographical distances. J Dairy Sci 2021; 104:2594-2605. [PMID: 33455775 DOI: 10.3168/jds.2020-19303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/10/2020] [Indexed: 12/18/2022]
Abstract
In the ecosystem of spontaneously fermented cow milk, the characteristics and relationship of bacterial communities and nonvolatile components at different scales of geographical distances (provincial, county, and village levels) are unclear. Here, 25 sampling sites from Xin Jiang and Tibet, 2 provinces of China, were selected based on the distribution of spontaneously fermented cow milk and used for metagenomic and metabolomic analysis. At the provincial geographical distance, the same predominant species, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus, were detected in Xin Jiang and Tibet. Further, the richness of the bacterial composition of samples from Tibet was higher than those from Xin Jiang; specifically, at the species level, 28 species were identified in Tibet samples but only 7 species in Xin Jiang samples. At the provincial geographical level, we detected significant differences in bacterial structure, shown in principal coordinate analysis plots, and significant differences (Simpson index) in bacterial diversity were also detected. However, at the county and village levels, no significant differences were detected in bacterial communities and diversity, but a difference in bacterial compositions was detectable. This indicates that bacterial communities and diversity of spontaneously fermented milk dissimilarity significantly increased with geographic distance. For the nonvolatile component profiles, the partial least squares discriminant analysis plot (R2Y > 0.5 and Q2 > 0.5 for the goodness-of-fit and predictive ability parameter, respectively) showed that samples from different geographical distances (provincial, county, and village) were all separated, which indicated that all the discriminations in nonvolatile components profiles were from different geographical distances. Investigating relationships between lactic acid bacteria and discriminatory nonvolatile components at the county level showed that 9 species were positively correlated with 16 discriminatory nonvolatile components, all species with low abundance rather than the predominant species L. delbrueckii ssp. bulgaricus and Strep. thermophilus, which indicates the importance of the selection of autochthonous nonpredominant bacteria.
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Affiliation(s)
- Chuantao Peng
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yaru Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
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18
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Yao G, He Q, Zhang W, Zhang H, Sun T. Single molecule, real-time sequencing technology improves the sensitivity for detecting bacteria in koumiss, a traditional fermented mare milk product. Sci Bull (Beijing) 2020; 65:2065-2067. [PMID: 36732957 DOI: 10.1016/j.scib.2020.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 07/14/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Guoqiang Yao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, 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
| | - Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, 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
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, 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.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, 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
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, 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.
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Adjunctive treatment with probiotics partially alleviates symptoms and reduces inflammation in patients with irritable bowel syndrome. Eur J Nutr 2020; 60:2553-2565. [PMID: 33225399 DOI: 10.1007/s00394-020-02437-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/04/2020] [Indexed: 01/01/2023]
Abstract
PURPOSE Irritable bowel syndrome (IBS) is a functional bowel disorder. This study aimed to assess the effect of a probiotic product (containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis subsp. lactis V9) as an adjunct to a routine regimen in IBS management. METHODS Forty-five patients with IBS were randomized into the probiotic (n = 24) and control (n = 21) groups, receiving the routine regimen with or without probiotics for 28 days, respectively. Serum and fecal samples were collected and analyzed. RESULTS The IBS-symptom severity score (P < 0.01), serum levels of IL-6 (P < 0.01) and TNF-α (P < 0.001) were significantly lower in the probiotic group than the control group at day 28. The probiotic adjunctive treatment resulted in significant decreases in some bacterial genera that worsen IBS, such as Bacteroides (P < 0.01), Escherichia (P < 0.05), and Citrobacter (P < 0.05), significant decreases were also observed in some beneficial genera in the control group, including Bifidobacterium (P < 0.05), Eubacterium (P < 0.05), Dorea (P < 0.01), and Butyricicoccus (P < 0.05). Furthermore, significant correlations were found between some monitored parameters and compositional changes in the fecal microbiota, suggesting that the clinical improvement of IBS was likely associated with gut microbiota modulation. The enterotype analysis revealed that the initial fecal microbiota composition could influence clinical outcomes. CONCLUSIONS The adjunctive use of probiotics with a routine regimen showed additional clinical effectiveness compared to the routine regimen alone in managing IBS. A pretreatment gut microbiome analysis might help tailor a personalized probiotic regimen to optimize treatment effects.
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20
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de Melo Pereira GV, de Carvalho Neto DP, Maske BL, De Dea Lindner J, Vale AS, Favero GR, Viesser J, de Carvalho JC, Góes-Neto A, Soccol CR. An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far? Crit Rev Food Sci Nutr 2020; 62:1870-1889. [PMID: 33207956 DOI: 10.1080/10408398.2020.1848787] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.
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Affiliation(s)
- Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Dão Pedro de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Bruna L Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Alexander S Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Gabriel R Favero
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Jéssica Viesser
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Júlio C de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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21
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Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee YK, Zhang H. Probiotic-directed modulation of gut microbiota is basal microbiome dependent. Gut Microbes 2020; 12:1736974. [PMID: 32200683 PMCID: PMC7524168 DOI: 10.1080/19490976.2020.1736974] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
As an effective means to improve quality of life and prevent diseases, the demand for probiotics and related products has increased in recent years. However, it is still unclear whether a particular probiotic strain will have similar beneficial effects on healthy adults from different regions. In this study, the probiotic Lactobacillus casei Zhang (LCZ) was consumed by healthy adults from six different Asian regions and the changes in gut microbiota were compared using PacBio single molecule, real-time (SMRT) sequencing technology based on samples collected before, during and after consumption of LCZ. Our results reveal that the effect of LCZ consumption on individuals was closely related to the composition of that individual's basal gut microbiota. A Gut Microbiota Variability Index (GMVI) was proposed to quantitatively compare the effects of LCZ on human gut microecology. Subjects from Xinjiang and Singapore regions had the highest and lowest GMVI, respectively. In general, consumption of LCZ increased the relative abundance of certain beneficial bacteria such as Lactobacillus, Roseburia, Coprococcus and Eubacterium rectale, while it inhibited growth of certain harmful bacteria such as Blautia and Ralstonia pickettii. In addition, consumption of LCZ was responsible for the conversion of some participants from Prevotella copri/Faecalibacterium prausnitzii (PF) enterotype to Faecalibacterium prausnitzii/Bacteroides dorei (FB) enterotype and consistently increased the abundance of lactic acid bacteria in the gut. It also increased/enhanced phosphate metabolic modules, amino acid transport systems, and isoleucine biosynthesis, but conversely decreased lipopolysaccharide biosynthesis. These changes could have health benefits for healthy adults.
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Affiliation(s)
- Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Feiyan Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Ruirui Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Wei Wei Thwe Khine
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jia Han
- Department of Nutrition and Food Hygiene, College of Public Health, Xinjiang Medical University, Urumqi, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China,CONTACT Heping Zhang Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot010018, China
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22
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Chen P, Xu H, Tang H, Zhao F, Yang C, Kwok L, Cong C, Wu Y, Zhang W, Zhou X, Zhang H. Modulation of gut mucosal microbiota as a mechanism of probiotics-based adjunctive therapy for ulcerative colitis. Microb Biotechnol 2020; 13:2032-2043. [PMID: 32969200 PMCID: PMC7533322 DOI: 10.1111/1751-7915.13661] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
This was a pilot study aiming to evaluate the effects of probiotics as adjunctive treatment for ulcerative colitis (UC). Twenty-five active patients with UC were assigned to the probiotic (n = 12) and placebo (n = 13) groups. The probiotic group received mesalazine (60 mg kg-1 day-1 ) and oral probiotics (containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8 and Bifidobacterium animalis subsp. lactis V9) twice daily for 12 weeks, while the placebo group received the same amounts of mesalazine and placebo. The clinical outcomes were assessed. The gut mucosal microbiota was profiled by PacBio single-molecule, real-time (SMRT) sequencing of the full-length 16S rRNA of biopsy samples obtained by colonoscopy. A significantly greater magnitude of reduction was observed in the UC disease activity index (UCDAI) in the probiotic group compared with the placebo group (P = 0.043), accompanying by a higher remission rate (91.67% for probiotic-receivers versus 69.23% for placebo-receivers, P = 0.034). The probiotics could protect from diminishing of the microbiota diversity and richness. Moreover, the gut mucosal microbiota of the probiotic-receivers had significantly more beneficial bacteria like Eubacterium ramulus (P < 0.05), Pediococcus pentosaceus (P < 0.05), Bacteroides fragilis (P = 0.02) and Weissella cibaria (P = 0.04). Additionally, the relative abundances of the beneficial bacteria correlated significantly but negatively with the UCDAI score, suggesting that the probiotics might alleviate UC symptoms by modulating the gut mucosal microbiota. Our research has provided new insights into the mechanism of symptom alleviation in UC by applying probiotic-based adjunctive treatment.
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Affiliation(s)
- Ping Chen
- The Affiliated Hospital of Inner Mongolia Medical UniversityHohhot010050China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
| | - Hai Tang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
| | - Feiyan Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
| | - Chengcong Yang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
| | - Lai‐Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
| | - Chunli Cong
- The Affiliated Hospital of Inner Mongolia Medical UniversityHohhot010050China
| | - YanFang Wu
- The Affiliated Hospital of Inner Mongolia Medical UniversityHohhot010050China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
| | | | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C.Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs P. R. C.Inner Mongolia Agricultural UniversityHohhot010018China
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Jingkai J, Jianming Z, Zhenmin L, Huaxi Y. Dynamic changes of microbiota and texture properties during the ripening of traditionally prepared cheese of China. Arch Microbiol 2020; 202:2059-2069. [PMID: 32488559 DOI: 10.1007/s00203-020-01921-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/13/2020] [Accepted: 05/25/2020] [Indexed: 10/24/2022]
Abstract
The dynamic changes of microbiota assessed by high-throughput sequencing and texture properties of handmade cheese were investigated during ripening time. Streptococcus and Lactococcus were found to be the most predominant genera. The proportion of Streptococcus was decreased from 48 to 32% and the proportion of Lactococcus was increased from 41 to 55% with ripening time from 1 to 120 days. Mould and yeast such as Paecilomyces, Candida, Issatchenkia, Rhodotorula, Cryptococcus and Trichosporon were observed. The regression analysis between composition and textural properties indicated that the hardness was increased along with the rising of soluble nitrogen, while the increased soluble nitrogen could result in lower cohesiveness, and the increased fat in dry matter resulted in lower resilience. The physic-chemical parameters were correlated with secondary microbiota such as Cryptococcus and Candida according to the multivariate association analysis (p < 0.05). These findings could provide a baseline to improve the product quality and preserve the traditional characteristics of handmade cheese.
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Affiliation(s)
- Jiao Jingkai
- State Key Laboratory of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 200436, China
| | - Zhang Jianming
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310016, Zhejiang, China
| | - Liu Zhenmin
- State Key Laboratory of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 200436, China
| | - Yi Huaxi
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266100, Shandong, China.
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24
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Fan H, Huo R, Zhao J, Zhou T, Zha M, Kwok LY, Zhang H, Chen Y. Microbial diversity analysis of jiaoke from Xilingol, Inner Mongolia. J Dairy Sci 2020; 103:5893-5905. [PMID: 32389475 DOI: 10.3168/jds.2019-17583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/03/2020] [Indexed: 11/19/2022]
Abstract
Jiaoke is a traditional Mongolian fermented dairy product that is nutritious and has a unique taste. It is made from the fat separated from fermented milk. In this study, we collected 24 jiaoke samples from the Xilingol region of Inner Mongolia. The microbiota composition of the collected samples was analyzed using 16S rRNA small-molecule real-time sequencing, and the lactic acid bacteria (LAB) population was enumerated and isolated by laboratory culture techniques. We used an electronic tongue device to assess the taste quality of the products. One hundred fifty LAB isolates (5 genera and 14 species) were recovered and identified by 16S rRNA sequencing across all samples. Lactococcus lactis and Lactobacillus plantarum accounted for 51.33% and 10.67% of the total isolates, respectively. The small-molecule real-time sequencing of full-length 16S rRNAs revealed an overall bacterial microbiota composition of 10 phyla, 121 genera, and 186 species, largely represented by sequences of Lactococcus (68.46%) and Lactococcus lactis (52.92%) at the genus and species levels, respectively. The electronic tongue analysis revealed that the sweetness, bitterness, sourness, and saltiness of jiaoke varied greatly between samples. The presence of Lactococcus lactis correlated positively with bitter aftertaste; the presence of Lactococcus piscium correlated positively with umami and negatively with astringent and bitter aftertastes; and the presence of Lactobacillus helveticus correlated positively with sourness and negatively with other taste qualities. These results suggest that the microbiota composition and product taste are closely related. The novel LAB strains collected in this work represent valuable natural microbial resources.
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Affiliation(s)
- Hui Fan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Rui Huo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jingna Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Tingting Zhou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Musu Zha
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
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25
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Kamilari E, Anagnostopoulos DA, Papademas P, Kamilaris A, Tsaltas D. Characterizing Halloumi cheese's bacterial communities through metagenomic analysis. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109298] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Tang H, Ma H, Hou Q, Li W, Xu H, Liu W, Sun Z, Haobisi H, Menghe B. Profiling of koumiss microbiota and organic acids and their effects on koumiss taste. BMC Microbiol 2020; 20:85. [PMID: 32276583 PMCID: PMC7149844 DOI: 10.1186/s12866-020-01773-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/29/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Koumiss is a naturally fermented mare's milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. RESULTS A total of 119 bacterial and 36 yeast species were identified among the 14 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactococcus raffinolactis, and Citrobacter freundii. The main yeast species were Dekkera anomala, Kazachstania unispora, Meyerozyma caribbica, Pichia sp.BZ159, Kluyveromyces marxianus, and uncultured Guehomyces. The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora, Dekkera anomala, and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami. CONCLUSIONS Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast species and taste also were found.
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Affiliation(s)
- Hai Tang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Huimin Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Halatu Haobisi
- Inner Mongolia International Mongolian Hospital, Hohhot, 010018, People's Republic of China
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
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Li R, Zheng X, Yang J, Shen X, Jiao L, Yan Z, Chen B, Han B. Relation Between Gut Microbiota Composition and Traditional Spontaneous Fermented Dairy Foods Among Kazakh Nomads in Xinjiang, China. J Food Sci 2019; 84:3804-3814. [PMID: 31750942 DOI: 10.1111/1750-3841.14912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
The human gastrointestinal tract represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation, as people from different regions have different gut microbiota structures. The Kazakh nomads in Xinjiang, China still retain their nomadic lifestyle and traditional diet. Their specific diet style and ancient genetic background shaped their gut microbiota to contain unique characteristics. In present study, the compositions of the gut microbiota and fermented dairy foods were assessed by high-throughput sequencing of the 16S rRNA gene. Twenty-nine Kazakh nomads were recruited, and 33 traditional fermented dairy foods were collected from five pasturing areas (Buerjin, Zhaosu, Nilka, Tekes, and Fuhai) in northern Xinjiang, China. The correlation of the physical index with the gut microbiota was also analyzed. The unique diet style of Kazakh may be a critical factor in keeping their gut microbiota in a balanced state and help them to remain in good health. PRACTICAL APPLICATION: This research shows that the consumption of spontaneous fermented dairy food plays an important role in increasing gut microbial diversity. Some probiotics in fermented dairy food, such as Bifidobacterium and Lactobacillus, have positive correlation with human body health index such as body mass index and blood glucose. These may provide some theoretical supports to adjuvant therapy of obesity and diabetes through scientific dietary intervention.
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Affiliation(s)
- Ruiyao Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural Univ., Beijing, China
| | - Xiaowei Zheng
- Biotechnology Center, Nutrition & Health Research Institute, COFCO Corp., Beijing, China.,Beijing Key Laboratory of Nutrition & Health and Food Safety, Beijing Engineering Laboratory for Geriatric Nutrition Food Research, Beijing, China
| | - Jie Yang
- College of Life Science and Technology, Xinjiang Univ., Urumqi, 830046, China
| | - Xuemei Shen
- Biotechnology Center, Nutrition & Health Research Institute, COFCO Corp., Beijing, China.,Beijing Key Laboratory of Nutrition & Health and Food Safety, Beijing Engineering Laboratory for Geriatric Nutrition Food Research, Beijing, China
| | - Lin Jiao
- Biotechnology Center, Nutrition & Health Research Institute, COFCO Corp., Beijing, China.,Beijing Key Laboratory of Nutrition & Health and Food Safety, Beijing Engineering Laboratory for Geriatric Nutrition Food Research, Beijing, China
| | - Zheng Yan
- College of Bioengineering, Beijing Polytechnic, Beijing, 100176, China
| | - Bo Chen
- Biotechnology Center, Nutrition & Health Research Institute, COFCO Corp., Beijing, China.,Beijing Key Laboratory of Nutrition & Health and Food Safety, Beijing Engineering Laboratory for Geriatric Nutrition Food Research, Beijing, China
| | - Beizhong Han
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural Univ., Beijing, China
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28
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Joishy TK, Dehingia M, Khan MR. Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk. World J Microbiol Biotechnol 2019; 35:102. [PMID: 31236715 DOI: 10.1007/s11274-019-2677-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/15/2019] [Indexed: 12/19/2022]
Abstract
Preparation of curd vary worldwide due to which its taste, texture and impact on human health also differ. In Assam, curd prepared from raw milk (RMC) is preferred over curd prepared from boiled milk (BMC), a tradition believed to have originated from the Mongoloid customs. Microbial diversity of raw milk (RM), boiled milk (BM), RMC and BMC collected from three farms were investigated by culture dependent and independent techniques. Additionally, metabolite profiles of RMC and BMC were studied by gas chromatography and mass spectroscopy. A total of 59 bacterial isolates were identified from the four different dairy products. In RM, lactic acid bacteria such as Lactococcus, Enterococcus, Lactobacillus and Leuconostoc were obtained along with the environmental bacteria like Bacillus, Staphylococcus, Acetobacter, Chryseobacterium, Streptococcus, Acinetobacter, Kocuria, Klebsiella and Macrococcus. Additionally, Prevotella, Oscillospira, Phascolarctobacterium and Akkermansia were also detected in BM by culture independent technique. In RMC and BMC, Lactococcus, Leuconostoc and Lactobacillus were prevalent. RM and RMC shared Enterococcus, Lactococcus, Streptococcus and Acinetobacter as common bacterial genera. However, no bacterial genus was common in BM and BMC. The correlation analysis revealed that Lactobacillus was negatively correlated to other bacterial genera. Oligotyping analysis revealed that Lactobacillus brevis and L.fermentum were abundant in RMC and BMC, respectively. In metabolomic study, ascorbic acid, dodecanoic acid and hexadecanoic acid were found to be significantly higher in RMC. Presence of different types of probiotics in these curds samples opens a new avenue to understand their effects on human health.
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Affiliation(s)
- Tulsi K Joishy
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.,Department of Molecular Biology and Biotechnology, Life Sciences Division, Cotton University, Guwahati, Assam, India
| | - Madhusmita Dehingia
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Mojibur R Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.
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29
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Milk and Dairy Products. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Mo L, Yu J, Jin H, Hou Q, Yao C, Ren D, An X, Tsogtgerel T, Zhang H. Investigating the bacterial microbiota of traditional fermented dairy products using propidium monoazide with single-molecule real-time sequencing. J Dairy Sci 2019; 102:3912-3923. [DOI: 10.3168/jds.2018-15756] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022]
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31
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Mo L, Jin H, Pan L, Hou Q, Li C, Darima I, Zhang H, Yu J. Biodiversity of lactic acid bacteria isolated from fermented milk products in Xinjiang, China. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2019.1574230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Lanxin Mo
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Hao Jin
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Lin Pan
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Chuanjuan Li
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Iaptueva Darima
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, P.R. China
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32
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Cao C, Hou Q, Hui W, Kwok L, Zhang H, Zhang W. Assessment of the microbial diversity of Chinese Tianshan tibicos by single molecule, real-time sequencing technology. Food Sci Biotechnol 2019; 28:139-145. [PMID: 30815304 DOI: 10.1007/s10068-018-0460-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/20/2018] [Accepted: 08/29/2018] [Indexed: 11/26/2022] Open
Abstract
Chinese Tianshan tibico grains were collected from the rural area of Tianshan in Xinjiang province, China. Typical tibico grains are known to consist of polysaccharide matrix that embeds a variety of bacteria and yeasts. These grains are widely used in some rural regions to produce a beneficial sugary beverage that is slightly acidic and contains low level of alcohol. This work aimed to characterize the microbiota composition of Chinese Tianshan tibicos using the single molecule, real-time sequencing technology, which is advantageous in generating long reads. Our results revealed that the microbiota mainly comprised of the bacterial species of Lactobacillus hilgardii, Lactococcus raffinolactis, Leuconostoc mesenteroides, Zymomonas mobilis, together with a Guehomyces pullulans-dominating fungal community. The data generated in this work helps identify beneficial microbes in Chinese Tianshan tibico grains.
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Affiliation(s)
- Chenxia Cao
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Qiangchuan Hou
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Wenyan Hui
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Laiyu Kwok
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Heping Zhang
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Wenyi Zhang
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
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33
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Hou Q, Li C, Liu Y, Li W, Chen Y, Siqinbateer, Bao Y, saqila W, Zhang H, Menghe B, Sun Z. Koumiss consumption modulates gut microbiota, increases plasma high density cholesterol, decreases immunoglobulin G and albumin. J Funct Foods 2019. [DOI: 10.1016/j.jff.2018.11.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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34
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Ma D, He Q, Ding J, Wang H, Zhang H, Kwok LY. Bacterial microbiota composition of fermented fruit and vegetable juices ( jiaosu) analyzed by single-molecule, real-time (SMRT) sequencing. CYTA - JOURNAL OF FOOD 2018. [DOI: 10.1080/19476337.2018.1512531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Da Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Jia Ding
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Huiyan Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
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35
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Yu J, Mo L, Pan L, Yao C, Ren D, An X, Tsogtgerel T, Zhang H, Liu W. Bacterial Microbiota and Metabolic Character of Traditional Sour Cream and Butter in Buryatia, Russia. Front Microbiol 2018; 9:2496. [PMID: 30459729 PMCID: PMC6232932 DOI: 10.3389/fmicb.2018.02496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/28/2018] [Indexed: 11/18/2022] Open
Abstract
Traditional sour cream and butter are widely popular fermented dairy products in Russia for their flavor and nutrition, and contain rich microbial biodiversity, particularly in terms of lactic acid bacteria (LAB). However, few studies have described the microbial communities and metabolic character of traditional sour cream and butter. The objective of this study was to determine the bacterial microbiota and metabolic character of eight samples collected from herdsmen in Buryatia, Russia. Using single-molecule real-time (SMRT) sequencing techniques, we identified a total of 294 species and/or subspecies in 169 bacterial genera, belonging to 14 phyla. The dominant phylum was Firmicutes (81.47%) and the dominant genus was Lactococcus (59.28%). There were differences between the bacterial compositions of the sour cream and butter samples. The relative abundances of Lactococcus lactis, Lactococcus raffinolactis, and Acetobacter cibinongensis were significantly higher in sour cream than in butter, and the abundance of Streptococcusthermophilus was significantly lower in sour cream than in butter. Using a pure culture method, 48 strains were isolated and identified to represent seven genera and 15 species and/or subspecies. Among these isolates, Lactococccus lactis subsp. lactis (22.50%) was the dominant LAB species. Ultra-performance liquid chromatography–quadrupole–time of flight mass spectrometry at elevated energy was used in combination with statistical methods to detect metabolite differences between traditional sour cream and butter. A total of 27,822 metabolites were detected in all samples, and Lys-Lys, isohexanal, palmitic acid, Leu-Val, and 2′-deoxycytidine were the most dominant metabolites found in all samples. In addition, 27 significantly different metabolites were detected between the sour cream and butter samples, including short peptides, organic acids, and amino acids. Based on correlation analyses between the most prevalent bacterial species and the main metabolites in sour cream, we conclude that there may be a connection between the dominant LAB species and these metabolites. This study combined omics techniques to analyze the bacterial diversity and metabolic character of traditional sour cream and butter, and we hope that our findings will enrich species resource libraries and provide valuable resources for further research on dairy product flavor.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Lanxin Mo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Lin Pan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Caiqing Yao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Dongyan Ren
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Xiaona An
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Tsedensodnom Tsogtgerel
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, China
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36
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Carafa I, Stocco G, Franceschi P, Summer A, Tuohy KM, Bittante G, Franciosi E. Evaluation of autochthonous lactic acid bacteria as starter and non-starter cultures for the production of Traditional Mountain cheese. Food Res Int 2018; 115:209-218. [PMID: 30599933 DOI: 10.1016/j.foodres.2018.08.069] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/10/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022]
Abstract
Lactococcus lactis subsp. lactis 68, Streptococcus thermophilus 93 and Lactobacillus rhamnosus BT68, previously isolated from Traditional Mountain (TM) cheese, were tested for the production of four experimental mountain cheeses, with the aim to assess their effectiveness in leading the TM-cheese-making process. Lactococcus lactis subsp. lactis 68 and Streptococcus thermophilus 93 were used as starter cultures, whereas Lactobacillus rhamnosus BT68 was used as non-starter culture. Three control (CTRL) cheeses were manufactured without adding any starter, according to the traditional cheese-making process; nine, cheeses were produced inoculating the vat milk with the starters (ST), starter and low concentration of non-starter culture (STLC), starter and high concentration of non-starter culture (STHC). Samples of vat milk, cheese after 24 h and 7 months ripening were processed for microbiological counts. Mesophilic cocci were dominant in all 24 h-cheese samples, while a dominance of both cocci and lactobacilli was observed after 7 months ripening. The total genomic DNA was extracted, and a fragment of V1-V3 region was amplified and pyrosequenced. Lactococci and streptococci were the most abundant species, and Lc. lactis ssp. lactis 68 affected the proliferation of milk-resident Lc. lactis ssp. cremoris, during the early fermentation. Lb. rhamnosus BT68 showed to be responsible in reducing the abundance of other Lactobacillus species. Moreover, it likely competed against Sc. thermophilus 93 for the same energetic sources, when added in concentration higher than 5 × 103 CFU/mL milk. The sensorial and fatty acid (FA) composition analysis were performed on cheese samples at the end of ripening, demonstrating that the inoculated cheeses had better sensorial characteristics (aspect, smell, taste, texture) than CTRL cheeses, and that Lb. rhamnosus BT68 at high concentration is related to the increase of short chain fatty acids and conjugated linoleic acid in cheese after 7 months ripening.
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Affiliation(s)
- Ilaria Carafa
- Research and Innovation Centre, AgriFood Quality and Nutrition Department, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Giorgia Stocco
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Piero Franceschi
- Department of Veterinary Science, University of Parma, Strada del Taglio, 10, 43126 Parma, Italy
| | - Andrea Summer
- Department of Veterinary Science, University of Parma, Strada del Taglio, 10, 43126 Parma, Italy
| | - Kieran Michael Tuohy
- Research and Innovation Centre, AgriFood Quality and Nutrition Department, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Elena Franciosi
- Research and Innovation Centre, AgriFood Quality and Nutrition Department, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all'Adige, Italy.
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Yang J, Cao J, Xu H, Hou Q, Yu Z, Zhang H, Sun Z. Bacterial diversity and community structure in Chongqing radish paocai brines revealed using PacBio single-molecule real-time sequencing technology. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:3234-3245. [PMID: 29417994 DOI: 10.1002/jsfa.8935] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Traditional Chongqing radish paocai fermented with aged brine is considered to have the most intense flavor and authentic taste. Eight 'Yanzhi' (red, RRPB group) and 'Chunbulao' (white, WRPB) radish paocai brine samples were collected from Chongqing peasant households, and the diversity and community structures of bacteria present in these brines were determined using PacBio single-molecule real-time sequencing of their full-length 16S rRNA genes. RESULTS In total, 30 phyla, 218 genera, and 306 species were identified from the RRPB group, with 20 phyla, 261 genera, and 420 species present in the WRPB group. Obvious differences in bacterial profiles between the RRPB and WRPB groups were found, with the bacterial diversity of the WRPB group shown to be greater than that of the RRPB group. This study revealed several characteristics of the bacteria composition, including the predominance of heterofermentative lactic acid bacteria, the species diversity of genus Pseudomonas, and the presence of three opportunistic pathogenic species. CONCLUSION This study provides detailed information on the bacterial diversity and community structure of Chongqing radish paocai brine samples, and suggests it may be necessary to analyze paocai brine for potential sources of bacterial contamination and take appropriate measures to exclude any pathogenic species. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jixia Yang
- Key laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, P. R. China
- College of Food Science, Southwest University, Tiansheng Road No.2, Beibei, Chongqing, P. R. China
| | - Jialu Cao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
| | - Haiyan Xu
- Key laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, P. R. China
| | - Qiangchuan Hou
- Key laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, P. R. China
| | - Zhongjie Yu
- Key laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, P. R. China
| | - Heping Zhang
- Key laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, P. R. China
| | - Zhihong Sun
- Key laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, P. R. China
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Mataragas M, Alessandria V, Ferrocino I, Rantsiou K, Cocolin L. A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods. Food Microbiol 2018; 76:279-286. [PMID: 30166151 DOI: 10.1016/j.fm.2018.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 11/29/2022]
Abstract
The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.
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Affiliation(s)
- Marios Mataragas
- Hellenic Agricultural Organization "DEMETER", Institute of Technology of Agricultural Products, Department of Dairy Research, Ethnikis Antistaseos 3, 45221, Ioannina, Greece.
| | - Valentina Alessandria
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Ilario Ferrocino
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Kalliopi Rantsiou
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Luca Cocolin
- University of Turin, Department of Agricultural, Forest and Food Sciences, Laboratory of Food Microbiology, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
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De Filippis F, Parente E, Ercolini D. Recent Past, Present, and Future of the Food Microbiome. Annu Rev Food Sci Technol 2018; 9:589-608. [DOI: 10.1146/annurev-food-030117-012312] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80131 Naples, Italy
| | - Eugenio Parente
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80131 Naples, Italy
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40
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Shangpliang HNJ, Rai R, Keisam S, Jeyaram K, Tamang JP. Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing. Sci Rep 2018; 8:1532. [PMID: 29367606 PMCID: PMC5784140 DOI: 10.1038/s41598-018-19524-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 01/04/2018] [Indexed: 01/11/2023] Open
Abstract
Naturally fermented milk (NFM) products are popular ethnic fermented foods in Arunachal Pradesh and Sikkim states of India. The present study is the first to have documented the bacterial community in 54 samples of NFM products viz. chhurpi, churkam, dahi and gheu/mar by high-throughput Illumina amplicon sequencing. Metagenomic investigation showed that Firmicutes (Streptococcaceae, Lactobacillaceae) and Proteobacteria (Acetobacteraceae) were the two predominant members of the bacterial communities in these products. Lactococcus lactis and Lactobacillus helveticus were the predominant lactic acid bacteria while Acetobacter spp. and Gluconobacter spp. were the predominant acetic acid bacteria present in these products.
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Affiliation(s)
- H Nakibapher Jones Shangpliang
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India
| | - Ranjita Rai
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India
| | - Santosh Keisam
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795 001, Manipur, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795 001, Manipur, India
| | - Jyoti Prakash Tamang
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India.
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41
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Wang Y, Guo J, Huang A. Study on bacterial diversity in traditional sour whey of Yunnan province. J FOOD PROCESS PRES 2017. [DOI: 10.1111/jfpp.13553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yujing Wang
- College of Food Science and Technology; Yunnan Agricultural University; Kunming Yunnan 650201, China
| | - Jie Guo
- College of Long Run Pu-erh Tea; Yunnan Agricultural University; Kunming 650201, China
| | - Aixiang Huang
- College of Food Science and Technology; Yunnan Agricultural University; Kunming Yunnan 650201, China
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Yu J, Ren Y, Xi X, Huang W, Zhang H. A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis. Front Microbiol 2017; 8:1782. [PMID: 29018412 PMCID: PMC5622921 DOI: 10.3389/fmicb.2017.01782] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/04/2017] [Indexed: 12/31/2022] Open
Abstract
Teat disinfection pre- and post-milking is important for the overall health and hygiene of dairy cows. The objective of this study was to evaluate the efficacy of a novel probiotic lactobacilli-based teat disinfectant based on changes in somatic cell count (SCC) and profiling of the bacterial community. A total of 69 raw milk samples were obtained from eleven Holstein-Friesian dairy cows over 12 days of teat dipping in China. Single molecule, real-time sequencing technology (SMRT) was employed to profile changes in the bacterial community during the cleaning protocol and to compare the efficacy of probiotic lactic acid bacteria (LAB) and commercial teat disinfectants. The SCC gradually decreased following the cleaning protocol and the SCC of the LAB group was slightly lower than that of the commercial disinfectant (CD) group. Our SMRT sequencing results indicate that raw milk from both the LAB and CD groups contained diverse microbial populations that changed over the course of the cleaning protocol. The relative abundances of some species were significantly changed during the cleaning process, which may explain the observed bacterial community differences. Collectively, these results suggest that the LAB disinfectant could reduce mastitis-associated bacteria and improve the microbial environment of the cow teat. It could be used as an alternative to chemical pre- and post-milking teat disinfectants to maintain healthy teats and udders. In addition, the Pacific Biosciences SMRT sequencing with the full-length 16S ribosomal RNA gene was shown to be a powerful tool for monitoring changes in the bacterial population during the cleaning protocol.
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Affiliation(s)
| | | | | | | | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
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43
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Kim IS, Hur YK, Kim EJ, Ahn YT, Kim JG, Choi YJ, Huh CS. Comparative analysis of the microbial communities in raw milk produced in different regions of Korea. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1643-1650. [PMID: 28935851 PMCID: PMC5666200 DOI: 10.5713/ajas.17.0689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 01/09/2023]
Abstract
Objective The control of psychrotrophic bacteria causing milk spoilage and illness due to toxic compounds is an important issue in the dairy industry. In South Korea, Gangwon-do province is one of the coldest terrains in which eighty percent of the area is mountainous regions, and mainly plays an important role in the agriculture and dairy industries. The purposes of this study were to analyze the indigenous microbiota of raw milk in Gangwon-do and accurately investigate a putative microbial group causing deterioration in milk quality. Methods We collected raw milk from the bulk tank of 18 dairy farms in the Hoengseong and Pyeongchang regions of Gangwon-do. Milk components were analyzed and the number of viable bacteria was confirmed. The V3 and V4 regions of 16S rRNA gene were amplified and sequenced on an Illumina Miseq platform. Sequences were then assigned to operational taxonomic units, followed by the selection of representative sequences using the QIIME software package. Results The milk samples from Pyeongchang were higher in fat, protein, lactose, total solid, and solid non-fat, and bacterial cell counts were observed only for the Hoengseong samples. The phylum Proteobacteria was detected most frequently in both the Hoengseong and Pyeongchang samples, followed by the phyla Firmicutes and Actinobacteria. Notably, Corynebacterium, Pediococcus, Macrococcus, and Acinetobacter were significantly different from two regions. Conclusion Although the predominant phylum in raw milk is same, the abundances of major genera in milk samples were different between Hoengseong and Pyeongchang. We assumed that these differences are caused by regional dissimilar farming environments such as soil, forage, and dairy farming equipment so that the quality of milk raw milk from Pyeongchang is higher than that of Hoengseong. These results could provide the crucial information for identifying the microbiota in raw milk of South Korea.
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Affiliation(s)
- In Seon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Yoo Kyung Hur
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Eun Ji Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Young-Tae Ahn
- R&BD Center, Korea Yakult Co., Ltd., Yongin 17086, Korea
| | - Jong Geun Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea.,Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute for Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
| | - Chul Sung Huh
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea.,Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
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44
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He GQ, Liu TJ, Sadiq FA, Gu JS, Zhang GH. Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches. J Zhejiang Univ Sci B 2017; 18:289-302. [PMID: 28378567 DOI: 10.1631/jzus.b1600148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
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Affiliation(s)
- Guo-Qing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Tong-Jie Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Faizan A Sadiq
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Si Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Hua Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
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45
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Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.02.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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46
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Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. Food Microbiol 2017; 68:129-136. [PMID: 28800820 DOI: 10.1016/j.fm.2017.07.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/13/2017] [Accepted: 07/16/2017] [Indexed: 11/22/2022]
Abstract
"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC.
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Hou N, Wen L, Cao H, Liu K, An X, Li D, Wang H, Du X, Li C. Role of psychrotrophic bacteria in organic domestic waste composting in cold regions of China. BIORESOURCE TECHNOLOGY 2017; 236:20-28. [PMID: 28390273 DOI: 10.1016/j.biortech.2017.03.166] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
To study the influence of psychrotrophic bacteria on organic domestic waste (ODW) composting in cold regions, twelve new efficient psychrotrophic composting strains were isolated. Together with the published representative composting strains, a phylogenetic tree was constructed showing that although the strains belong to the same phylum, the genera were markedly different. The twelve strains were inoculated into the ODW in the composting reactor at 13°C. After treatment, the indices of temperature, moisture content, pH, electrical conductivity, C/N, ammonium nitrogen, and nitrate nitrogen indicated that the compost had reached maturity. The thermophilic phase was reached at 17d, and composting was completed at 42d, a markedly shorter composting time than that in previous studies. High-throughput sequencing indicated that the inoculative strains became the dominant community during the mesophilic phase and that they enhanced the stability of the microbial community structure. Thus, psychrotrophic bacteria played a key role in low-temperature composting.
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Affiliation(s)
- Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Luming Wen
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Huiming Cao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Keran Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xuejiao An
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Dapeng Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Hailan Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xiaopeng Du
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
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48
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Ferrocino I, Cocolin L. Current perspectives in food-based studies exploiting multi-omics approaches. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.01.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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49
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Li J, Zheng Y, Xu H, Xi X, Hou Q, Feng S, Wuri L, Bian Y, Yu Z, Kwok LY, Sun Z, Sun T. Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses. BMC Microbiol 2017; 17:13. [PMID: 28068902 PMCID: PMC5223556 DOI: 10.1186/s12866-016-0911-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 12/10/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy. RESULTS Across the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference. CONCLUSION Our results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal cheeses of various geographical origins.
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Affiliation(s)
- Jing Li
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Yi Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Shuzhen Feng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Laga Wuri
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Yanfei Bian
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhongjie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
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50
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Zhao L, Li Y, Jiang L, Deng F. Determination of fungal community diversity in fresh and traditional Chinese fermented pepper by pyrosequencing. FEMS Microbiol Lett 2016; 363:fnw273. [DOI: 10.1093/femsle/fnw273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/26/2016] [Accepted: 12/05/2016] [Indexed: 11/13/2022] Open
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