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De Filippis F, Parente E, Ercolini D. Metagenomics insights into food fermentations. Microb Biotechnol 2016; 10:91-102. [PMID: 27709807 PMCID: PMC5270737 DOI: 10.1111/1751-7915.12421] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 11/26/2022] Open
Abstract
This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.
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Affiliation(s)
- Francesca De Filippis
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Li J, Xu H, Sun Z, Hou Q, Kwok LY, Laga W, Wang Y, Ma H, Yu Z, Menghe B, Zhang H. Effect of dietary interventions on the intestinal microbiota of Mongolian hosts. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1173-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Zhong Z, Hou Q, Kwok L, Yu Z, Zheng Y, Sun Z, Menghe B, Zhang H. Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type. J Dairy Sci 2016; 99:7832-7841. [DOI: 10.3168/jds.2015-10825] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/02/2016] [Indexed: 11/19/2022]
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Zheng Y, Xi X, Xu H, Hou Q, Bian Y, Yu Z, Kwok LY, Zhang W, Sun Z, Zhang H. Using PacBio Long-Read High-Throughput Microbial Gene Amplicon Sequencing To Evaluate Infant Formula Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:6993-7001. [PMID: 27500310 DOI: 10.1021/acs.jafc.6b01817] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Infant formula (IF) requires a strict microbiological standard because of the high vulnerability of infants to foodborne diseases. The current study used the PacBio single-molecule real-time (SMRT) sequencing platform to generate full-length 16S rRNA-based bacterial microbiota profiles of 30 Chinese domestic and imported IF samples. A total of 600 species were identified, dominated by Streptococcus thermophilus, Lactococcus lactis, and Lactococcus piscium. Distinctive bacterial profiles were observed between the two sample groups, as confirmed with both principal coordinate analysis and multivariate analysis of variance. Moreover, the product whey protein nitrogen index (WPNI), representing the degree of preheating, negatively correlated with the relative abundances of the Bacillus genus. This study has demonstrated the application of the PacBio SMRT sequencing platform in assessing the bacterial contamination of IF products, which is of interest to the dairy industry for effective monitoring of microbial quality and safety during production.
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Affiliation(s)
- Yi Zheng
- 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
| | - Haiyan Xu
- 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
| | - 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
| | - Wenyi Zhang
- 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
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University , Hohhot 010018, People's Republic of China
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Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food. Sci Rep 2016; 6:32524. [PMID: 27578483 PMCID: PMC5006176 DOI: 10.1038/srep32524] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/10/2016] [Indexed: 11/23/2022] Open
Abstract
Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample.
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Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters. Sci Rep 2016; 6:28358. [PMID: 27340760 PMCID: PMC4920031 DOI: 10.1038/srep28358] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/01/2016] [Indexed: 01/03/2023] Open
Abstract
The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.
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Analysis of the microbial diversity in faecal material of the endangered blue whale, Balaenoptera musculus. Antonie van Leeuwenhoek 2016; 109:1063-9. [DOI: 10.1007/s10482-016-0698-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
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Hou Q, Xu H, Zheng Y, Xi X, Kwok LY, Sun Z, Zhang H, Zhang W. Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology. J Dairy Sci 2015; 98:8464-72. [PMID: 26476945 DOI: 10.3168/jds.2015-9886] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/28/2015] [Indexed: 01/07/2023]
Abstract
The Pacific Biosciences (Menlo Park, CA) single molecule, real-time sequencing technology (SMRT) was reported to have some advantages in analyzing the bacterial profile of environmental samples. In this study, the presence of bacterial contaminants in raw milk, UHT milk, and infant formula was determined by SMRT sequencing of the full length 16S rRNA gene. The bacterial profiles obtained at different taxonomic levels revealed clear differences in bacterial community structure across the 16 analyzed dairy samples. No indicative pathogenic bacteria were found in any of these tested samples. However, some of the detected bacterial species (e.g., Bacillus cereus, Enterococcus casseliflavus, and Enterococcus gallinarum) might potentially relate with product quality defects and bacterial antibiotic gene transfer. Although only a limited number of dairy samples were analyzed here, our data have demonstrated for the first time the feasibility of using the SMRT sequencing platform in detecting bacterial contamination. Our paper also provides interesting reference information for future development of new precautionary strategies for controlling the dairy safety in large-scale industrialized production lines.
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Affiliation(s)
- Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Yi Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
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