Metagenomic insights into the bacteria responsible for producing biogenic amines in sufu

Ahmad, 2019, Biogenic amines formation mechanism and determination strategies: future challenges and limitations, Crit. Rev. Anal. Chem., 1 Alberto, 2007, Putrescine production from agmatine by Lactobacillus hilgardii: effect of phenolic compounds, Food Contr., 18, 898, 10.1016/j.foodcont.2006.05.006 Alneberg, 2014, Binning metagenomic contigs by coverage and composition, Nat. Methods, 11, 1144, 10.1038/nmeth.3103 Alvarez, 2014, The problem of biogenic amines in fermented foods and the use of potential biogenic amine-degrading microorganisms as a solution, Trends Food Sci. Technol., 39, 146, 10.1016/j.tifs.2014.07.007 Barbieri, 2019, Biogenic amine production by lactic acid bacteria: a review, Foods, 8, 17, 10.3390/foods8010017 Björnsdóttir-Butler, 2010, Development of molecular-based methods for determination of high histamine producing bacteria in fish, Int. J. Food Microbiol., 139, 161, 10.1016/j.ijfoodmicro.2010.03.017 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Chen, 2018, Potential probiotic characterization of Lactobacillus reuteri from traditional Chinese highland barley wine and application for room-temperature-storage drinkable yogurt, J. Dairy Sci., 101, 5780, 10.3168/jds.2017-14139 De Filippis, 2017, Metagenomics insights into food fermentations, Microbial Biotechnology, 10, 91, 10.1111/1751-7915.12421 EFSA, 2011, Scientific Opinion on risk based control of biogenic amine formation in fermented foods, EFSA Journal, 9, 2393, 10.2903/j.efsa.2011.2393 Franzosa, 2018, Species-level functional profiling of metagenomes and metatranscriptomes, Nat. Methods, 15, 962, 10.1038/s41592-018-0176-y Gardini, 2016, Technological factors affecting biogenic amine content in foods: a review, Front. Microbiol., 7, 1218, 10.3389/fmicb.2016.01218 GB, 2016 Guan, 2013, Investigation of biogenic amines in sufu (furu): a Chinese traditional fermented soybean food product, Food Contr., 31, 345, 10.1016/j.foodcont.2012.10.033 Han, 2001, Microbiological safety and quality of commercial sufu – a Chinese fermented soybean food, Food Contr., 12, 541, 10.1016/S0956-7135(01)00064-0 Huang, 2018, Bacterial community succession and metabolite changes during sufu fermentation, LWT-Food Science and Technology, 97, 537, 10.1016/j.lwt.2018.07.041 Huson, 2007, MEGAN analysis of metagenomic data, Genome Res., 17, 377, 10.1101/gr.5969107 Hwan, 1999, Volatile components of the Chinese fermented soya bean curd as affected by the addition of ethanol in ageing solution, J. Sci. Food Agric., 79, 243, 10.1002/(SICI)1097-0010(199902)79:2<243::AID-JSFA179>3.0.CO;2-I Kanehisa, 2000, KEGG: Kyoto encyclopedia of genes and genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27 Ladero, 2012, Multiplex qPCR for the detection and quantification of putrescine-producing lactic acid bacteria in dairy products, Food Contr., 27, 307, 10.1016/j.foodcont.2012.03.024 Ladero, 2010, qPCR for quantitative detection of tyramine-producing bacteria in dairy products, Food Res. Int., 43, 289, 10.1016/j.foodres.2009.10.007 Landete, 2011, PCR methods for the detection of biogenic amine-producing bacteria on wine, Ann. Microbiol., 61, 159, 10.1007/s13213-010-0068-6 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Li, 2019, Occurrence of biogenic amines in sufu obtained from Chinese market, Food Science and Biotechnology, 28, 319, 10.1007/s10068-018-0500-4 Liang, 2019, Effects of different co-cultures on the amino acid availability, biogenic amine concentrations and protein metabolism of fermented sufu and their relationships, LWT-Food Science and Technology, 113, 108323, 10.1016/j.lwt.2019.108323 Lorenzo, 2019, Controlling biogenic amine formation in food, 41 Mohedano, 2015, Controlling the formation of biogenic amines in fermented foods, 273 Nishino, 2007, Biogenic amine production in grass, maize and total mixed ration silages inoculated with Lactobacillus casei or Lactobacillus buchneri, J. Appl. Microbiol., 103, 325, 10.1111/j.1365-2672.2006.03244.x O'Sullivan, 2015, High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses, BMC Microbiol., 15, 266, 10.1186/s12866-015-0596-0 Parks, 2015, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res., 25, 1043, 10.1101/gr.186072.114 Peng, 2012, IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420, 10.1093/bioinformatics/bts174 Rho, 2010, FragGeneScan: predicting genes in short and error-prone reads, Nucleic Acids Res., 38, 10.1093/nar/gkq747 Rolfe, 2020, Intrinsic and extrinsic factors affecting microbial growth in food systems, 3 Romano, 2014, Putrescine production via the ornithine decarboxylation pathway improves the acid stress survival of Lactobacillus brevis and is part of a horizontally transferred acid resistance locus, Int. J. Food Microbiol., 175, 14, 10.1016/j.ijfoodmicro.2014.01.009 Rossi, 2011, Quantitative analysis of histidine decarboxylase gene hdcA transcription and histamine production by Streptococcus thermophilus PRI60 under conditions relevant to cheese making, Appl. Environ. Microbiol., 77, 2817, 10.1128/AEM.02531-10 Sahu, 2016, Biogenic amines in fermented foods: Overview, vol. 1, 303 Santos, 1996, Biogenic amines: their importance in foods, Int. J. Food Microbiol., 29, 213, 10.1016/0168-1605(95)00032-1 Segata, 2013, PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes, Nat. Commun., 4, 2304, 10.1038/ncomms3304 Tan, 2020, High-throughput sequencing and metabolomics reveal differences in bacterial diversity and metabolites between red and white sufu, Front. Microbiol., 11, 758, 10.3389/fmicb.2020.00758 Tang, 2011, Monitoring the contents of biogenic amines in sufu by HPLC with SPE and pre-column derivatization, Food Contr., 22, 1203, 10.1016/j.foodcont.2011.01.018 Tittarelli, 2019, Biogenic amines producing and degrading bacteria: a snapshot from raw ewes' cheese, LWT-Food Science and Technology, 101, 1, 10.1016/j.lwt.2018.11.030 US Food and Drug Administration, 2001, 73 Wunderlichová, 2013, Novel touchdown-PCR method for the detection of putrescine producing gram-negative bacteria in food products, Food Microbiol., 34, 268, 10.1016/j.fm.2012.09.024