基于宏基因组测序对中国北方地区生乳中嗜冷菌的群落结构研究

doi:10.11843/j.issn.0366-6964.2024.08.037

Abstract

Abstract:

The aim of this study was to investigate the community structure diversity of psychrophilic bacteria in raw milk in northern China by metagenomic sequencing. A total of 14 raw milk samples were collected from 14 pastures in Inner Mongolia and Beijing, China in winter. The culturable psychrophilic bacteria were isolated and purified, total microbial DNA in raw milk was extracted as well. Moreover, the psychrophilic bacteria in raw milk were analyzed by 16S rDNA sequencing and metagenomic sequencing, respectively. The results showed that no significant difference was found in community structure of psychrophilic bacteria in raw milk between Beijing and Inner Mongolia. Pseudomonas, Stenotrophomonas and Brevundimonas were the dominant psychrophiles bacteria in raw milk from the two regions. The global and overview profiles, amino acid metabolism and carbohydrate metabolism were the most important functional metabolic pathways, and psychrophilic bacteria contained a variety of antibiotic resistance genes. In conclusion, this study used traditional culture and metagenomic sequencing to accurately determine the species and functional information of the psychrophilic community in raw milk, which is helpful to understand the life activities of psychrophilic bacteria in raw milk and provide basic information for risk assessment of psychrophilic bacteria. Furthermore, it lays down foundational knowledge pivotal for the effective prevention and management of pasture-related issues in Beijing and Inner Mongolia, China.

Key words: raw milk, psychrophilic bacteria, metagenomic sequencing, region, structure

CLC Number:

TS252.1

Wenjun XU, Nan ZHENG, Jiaqi WANG, Lu MENG. Study on the Community Structure of Psychrophilic Bacteria in Raw Milk from North Regions of China based on Metagenomic Sequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(8): 3659-3668.

Figures/Tables 9

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References 30

1	YUAN L , SADIQ F A , BURMOLLE M , et al. Insights into psychrotrophic bacteria in raw milk: a review[J]. J Food Prot, 2019, 82 (7): 1148- 1159. doi: 10.4315/0362-028X.JFP-19-032
2	DOGAN B , BOOR K J . Genetic diversity and spoilage potentials among Pseudomonas spp. isolated from fluid milk products and dairy processing plants[J]. Appl Environ Microbiol, 2003, 69 (1): 130- 138. doi: 10.1128/AEM.69.1.130-138.2003
3	JIN S S , WANG Y Z , ZHAO X H . Cold-adaptive mechanism of psychrophilic bacteria in food and its application[J]. Microb Pathog, 2022, 169, 105652. doi: 10.1016/j.micpath.2022.105652
4	QUIGLEY L , O'SULLIVAN O , STANTON C , et al. The complex microbiota of raw milk[J]. FEMS Microbiol Rev, 2013, 37 (5): 664- 698. doi: 10.1111/1574-6976.12030
5	KIM I S , HUR Y K , KIM E J , et al. Comparative analysis of the microbial communities in raw milk produced in different regions of Korea[J]. Asian-Australas J Anim Sci, 2017, 30 (11): 1643- 1650. doi: 10.5713/ajas.17.0689
6	YUAN L , SADIQ F A , LIU T J , et al. Spoilage potential of psychrotrophic bacteria isolated from raw milk and the thermo-stability of their enzymes[J]. J Zhejiang Univ Sci B, 2018, 19 (8): 630- 642. doi: 10.1631/jzus.B1700352
7	SAMARŽIJA D , ZAMBERLIN Š , POGAČIĆ T . Psychrotrophic bacteria and milk and dairy products quality[J]. Mljekarstvo, 2012, 62 (2): 77- 95.
8	MARTIN N H , ORRES-FRENZEL P , WIEDMANN M . Invited review: Controlling dairy product spoilage to reduce food loss and waste[J]. J Dairy Sci, 2021, 104 (2): 1251- 1261. doi: 10.3168/jds.2020-19130
9	OUAMBA A J K , GAGNON M , LAPOINTE G , et al. Graduate Student Literature Review: Farm management practices: Potential microbial sources that determine the microbiota of raw bovine milk[J]. J Dairy Sci, 2022, 105 (9): 7276- 7287. doi: 10.3168/jds.2021-21758
10	YAP M , GLEESON D , O'TOOLE P W , et al. Seasonality and geography have a greater influence than the use of chlorine-based cleaning agents on the microbiota of bulk tank raw milk[J]. Appl Environ Microbiol, 2021, 87 (22): e01081- 21.
11	GUO X C , YU Z J , ZHAO F Y , et al. Both sampling seasonality and geographic origin contribute significantly to variations in raw milk microbiota, but sampling seasonality is the more determining factor[J]. J Dairy Sci, 2021, 104 (10): 10609- 10627. doi: 10.3168/jds.2021-20480
12	LIANG L J , WANG P , ZHAO X M , et al. Single-molecule real-time sequencing reveals differences in bacterial diversity in raw milk in different regions and seasons in China[J]. J Dairy Sci, 2022, 105 (7): 5669- 5684. doi: 10.3168/jds.2021-21445
13	FRANZOSA E A , HSU T , SIROTA-MADI A , et al. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling[J]. Nat Rev Microbiol, 2015, 13 (6): 360- 372. doi: 10.1038/nrmicro3451
14	WANG J C , ZHENG Y , XI X X , et al. Application of PacBio Single Molecule Real-Time (SMRT) sequencing in bacterial source tracking analysis during milk powder production[J]. Food Control, 2018, 93, 226- 234. doi: 10.1016/j.foodcont.2018.05.044
15	CHEN S F , ZHOU Y Q , CHEN Y R , et al. fastp: an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34 (17): i884- i890. doi: 10.1093/bioinformatics/bty560
16	LI H , DURBIN R . Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25 (14): 1754- 1760. doi: 10.1093/bioinformatics/btp324
17	REN Y , YU G , SHI C P , et al. Majorbio Cloud: A one-stop, comprehensive bioinformatic platform for multiomics analyses[J]. iMeta, 2022, 1 (2): e12. doi: 10.1002/imt2.12
18	ZHANG D , LI S Q , PALMER J , et al. The relationship between numbers of Pseudomonas bacteria in milk used to manufacture UHT milk and the effect on product quality[J]. Int Dairy J, 2020, 105, 104687. doi: 10.1016/j.idairyj.2020.104687
19	ZHANG D , PALMER J , TEH K H , et al. Identification and selection of heat-stable protease and lipase-producing psychrotrophic bacteria from fresh and chilled raw milk during up to five days storage[J]. LWT, 2020, 134, 110165. doi: 10.1016/j.lwt.2020.110165
20	YANG X Y , GUO X J , LIU W P , et al. The complex community structures and seasonal variations of psychrotrophic bacteria in raw milk in Heilongjiang Province, China[J]. LWT, 2020, 134, 110218. doi: 10.1016/j.lwt.2020.110218
21	DU B Y , MENG L , LIU H M , et al. Single molecule real-time sequencing and traditional cultivation techniques reveal complex community structures and regional variations of psychrotrophic bacteria in raw milk[J]. Front Microbiol, 2022, 13, 853263. doi: 10.3389/fmicb.2022.853263
22	NARVHUS J A , BÆKKELUND O N , TIDEMANN E M , et al. Isolates of Pseudomonas spp. from cold-stored raw milk show variation in proteolytic and lipolytic properties[J]. Int Dairy J, 2021, 123, 105049. doi: 10.1016/j.idairyj.2021.105049
23	RUEGG P L . A 100-Year Review: Mastitis detection, management, and prevention[J]. J Dairy Sci, 2017, 100 (12): 10381- 10397.
24	DU B Y , MENG L , LIU H M , et al. Impacts of milking and housing environment on milk microbiota[J]. Animals (Basel), 2020, 10 (12): 2339.
25	JIANG Y , YU P , LIU X M , et al. Shifts in diversity and function of bacterial community during manufacture of rushan[J]. J Dairy Sci, 2021, 104 (12): 12375- 12393.
26	胡海燕, 刘慧敏, 孟璐, 等. 宏基因组学在微生物抗生素抗性基因检测中的应用[J]. 微生物学通报, 2019, 46 (11): 3110- 3123.
	HU H Y , LIU H M , MENG L , et al. Application of metagenomics in the detection of microbial antibiotic resistance genes[J]. Microbiology China, 2019, 46 (11): 3110- 3123.
27	TÓTH A G , CSABAI I , KRIKÓ E , et al. Antimicrobial resistance genes in raw milk for human consumption[J]. Sci Rep, 2020, 10 (1): 7464.
28	MENG L , LIU H M , LAN T , et al. Antibiotic resistance patterns of Pseudomonas spp. isolated from raw milk revealed by whole genome sequencing[J]. Front Microbiol, 2020, 11, 1005.
29	LIU J X , ZHU Y T , JAY-RUSSELL M , et al. Reservoirs of antimicrobial resistance genes in retail raw milk[J]. Microbiome, 2020, 8 (1): 99.
30	PATEL K , AMARESAN N . Antimicrobials compounds from extreme environment Rhizosphere organisms for plant growth[J]. Int J Curr Microbiol App Sci, 2014, 3 (7): 651- 664.

引物 Primer	序列 Sequence	参考文献 Reference
27F	AGAGTTTGATCMTGGCTCAG	[14]
1492R	GGTTACCTTGTTACGACTT

属 Genera	种 Species	总数(株) Total number (strains)	北京地区 Beijing	内蒙古地区 Inner Mongolia
Acinetobacter	albensis	1	0	1
	sp. TAC-1	1	0	1
Arthrobacter	alpinus	1	1	0
Carnobacterium	maltaromaticum	1	1	0
Chryseobacterium	balustinum	1	0	1
	indoltheticum	2	1	1
	sp. Sin57	2	2	0
	sp. WW-RP1	1	0	1
	vrystaatense	1	0	1
	yeoncheonense	1	1	0
Flavobacterium	sp. F-340	1	0	1
Glutamicibacter	bergerei	1	0	1
Lactococcus	carnosus	1	1	0
Paeniglutamicibacter	antarcticus	1	0	1
Pseudomonas	azotoformans	1	1	0
	cedrina	1	0	1
	fluorescens	3	1	2
	gessardii	3	2	1
	mandelii	1	0	1
	paralactis	1	1	0
	poae	1	1	0
	rhodesiae	1	0	1
	sp. HW08	2	2	0
Psychrobacter	faecalis	1	1	0
	pulmonis	5	2	3
	sp. S06	2	0	2
	sp. SOD-1301	1	0	1
Serratia	liquefaciens	4	2	2
	grimesii	2	1	1

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Study on the Community Structure of Psychrophilic Bacteria in Raw Milk from North Regions of China based on Metagenomic Sequencing

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