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Werum V, Ehrmann M. Transcriptome responses of Lactococcus paracarnosus to different gas compositions and co-culture with Brochothrix thermosphacta. Int J Food Microbiol 2024; 421:110803. [PMID: 38908220 DOI: 10.1016/j.ijfoodmicro.2024.110803] [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: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
Lactococcus (Lc.) paracarnosus and the phylogenetically closely related Lc. carnosus species are common members of the microbiota in meat stored under modified atmosphere and at low temperature. The effect of these strains on meat spoilage is controversially discussed. While some strains are known to cause spoilage, others are being studied for their potential to suppress the growth of spoilage and pathogenic bacteria. In this study, Lc. paracarnosus DSM 111017T was selected based on a previous study for its ability to suppress the growth of meat spoilers, including Brochothrix thermosphacta. The mechanism by which this bioprotective strain inhibits competing bacteria and how it contributes to spoilage are not yet known. To answer these two questions, we investigated the effect of four different headspace gas mixtures (simulated air (21 % O2/79 % N2); HiOx-MAP (70 % O2/30 % CO2); nonOx-MAP (70 % N2/ 30 % CO2); simulated vacuum (100 % N2) and the presence of Brochothrix (B.) thermosphacta TMW 2.2101 on the growth and transcriptional response of Lc. paracarnosus DSM 111017T when cultured on a meat simulation agar surface at 4 °C. Analysis of genes specifically upregulated by the gas mixtures used revealed metabolic pathways that may lead to different levels of spoilage metabolites production. We propose that under elevated oxygen levels, Lc. paracarnosus preferentially converts pyruvate from glucose and glycerol to uncharged acetoin/diacetyl instead of lactate to counteract acid stress. Due to the potential production of a buttery off-flavour, the strain may not be suitable as a protective culture in meat packaged under high‑oxygen conditions. 70 % N2/ 30 % CO2, simulated vacuum- and the presence of Lc. paracarnosus inhibited the growth of B. thermosphacta TMW 2.2101. However, B. thermosphacta did not affect gene regulation of metabolic pathways in Lc. paracarnosus, and genes previously predicted to be involved in B. thermosphacta growth suppression were not regulated at the transcriptional level. In conclusion, the study indicates that the gas mixture used in packaging significantly affects the metabolism and spoilage potential of Lc. paracarnosus and its ability to inhibit B. thermosphacta growth.
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Affiliation(s)
- Victoria Werum
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Matthias Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany.
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2
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Zhao L, Li X, Wang Y, Yang Q, Jiang X, Zhao R, Chen H, Zhang Y, Ran J, Chen W, Wei Z, Wang H. Resistance role of Lactobacillus sp. and Lactococcus sp. to copper ions in healthy children's intestinal microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134059. [PMID: 38503209 DOI: 10.1016/j.jhazmat.2024.134059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/10/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Heavy metal exposure is closely associated with gut microbe function and tolerance. However, intestinal microbe responses in children to different copper ion (Cu2+) concentrations have not yet been clarified. Here, in vitro cultivation systems were established for fecal microbe control and Cu2+-treated groups in healthy children. 16S rDNA high-throughput sequencing, meta-transcriptomics and metabolomics were used here to identify toxicity resistance mechanisms at microbiome levels. The results showed that Lactobacillus sp. and Lactococcus sp. exerted protective effects against Cu2+ toxicity, but these effects were limited by Cu2+ concentration. When the Cu2+ concentration was ≥ 4 mg/L, the abundance of Lactobacillus sp. and Lactococcus sp. significantly decreased, and the pathways of antioxidant activity and detoxification processes were enriched at 2 mg/L Cu2+, and beneficial metabolites accumulated. However, at high concentrations of Cu2+ (≥4 mg/L), the abundance of potential pathogen increased, and was accompanied by a downregulation of genes in metabolism and detoxification pathways, which meant that the balance of gut microbiota was disrupted and toxicity resistance decreased. From these observations, we identified some probiotics that are tolerant to heavy metal Cu2+, and warn that only when the concentration limit of Cu2+ in food is 2 mg/L, then a balanced gut microbiota can be guaranteed in children, thereby providing protection for their health.
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Affiliation(s)
- Lili Zhao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xinlei Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Yibin Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China.
| | - Xiaobing Jiang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
| | - Ruixiang Zhao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Hong Chen
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Yiping Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Junjian Ran
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Wanrong Chen
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Zihan Wei
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Hailei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
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Seibt ACMD, Nerhing P, Pinton MB, Santos SP, Leães YSV, De Oliveira FDC, Robalo SS, Casarin BC, Dos Santos BA, Barin JS, Wagner R, De Menezes CR, Campagnol PCB, Cichoski AJ. Green technologies applied to low-NaCl fresh sausages production: Impact on oxidative stability, color formation, microbiological properties, volatile compounds, and sensory profile. Meat Sci 2024; 209:109418. [PMID: 38113656 DOI: 10.1016/j.meatsci.2023.109418] [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: 08/22/2023] [Revised: 11/24/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
The influence of different concentrations of NaCl (2.5% and 1.75%), basic electrolyzed water (BEW), and ultrasound (US, 25 kHz, 159 W) on the quality of fresh sausages was studied. During storage at 5 °C, TBARS, pH, Eh, aw, nitrous pigments, and bacterial evolution were evaluated at three specific time intervals: 1d, 15d, and 30d. At the same time, the volatile compounds and sensory profile were specifically assessed on both the 1d and 30d. Notably, sausages with 1.75% NaCl and BEW displayed higher pH values (up to 6.30) and nitrous pigment formation, alongside reduced Eh (as low as 40.55 mV) and TBARS values (ranging from 0.016 to 0.134 mg MDA/kg sample), compared to the 2.5% NaCl variants. Protein content ranged between 13.01% and 13.75%, while lipid content was between 18.23% and 18.86%, consistent across all treatments. Psychrotrophic lactic bacteria showed a significant increase in low-NaCl sausages, ranging from 5.77 to 7.59 log CFU/g, indicative of potential preservative benefits. The sensory analysis favored the TUSBEW70 treatment for its salty flavor on the 30th day, reflecting a positive sensory acceptance. The study highlights that employing US and BEW in sausage preparation with reduced NaCl content (1.75%) maintains quality comparable to higher salt (2.5%) counterparts. These findings are crucial for meat processing, presenting a viable approach to producing healthier sausages with reduced sodium content without compromising quality, aligning with consumer health preferences and industry standards.
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Affiliation(s)
| | - Priscila Nerhing
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Mariana Basso Pinton
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Suelen Priscila Santos
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Yasmim Sena Vaz Leães
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | | | - Silvino Sasso Robalo
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Bianca Campos Casarin
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | | | - Juliano Smanioto Barin
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Roger Wagner
- Universidade Federal de Santa Maria, CEP 97105-900 Santa Maria, Rio Grande do Sul, Brazil
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Hung CC, Chao YP, Lee Y, Huang CW, Huang SH, Chang CC, Cheng CH. Cingulate white matter mediates the effects of fecal Ruminococcus on neuropsychiatric symptoms in patients with amyloid-positive amnestic mild cognitive impairment. BMC Geriatr 2023; 23:720. [PMID: 37936084 PMCID: PMC10631051 DOI: 10.1186/s12877-023-04417-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Microbiota-gut-brain axis interacts with one another to regulate brain functions. However, whether the impacts of gut dysbiosis on limbic white matter (WM) tracts contribute to the neuropsychiatric symptoms (NPS) in patients with amyloid-positive amnestic mild cognitive impairment (aMCI+), have not been explored yet. This study aimed to investigate the mediation effects of limbic WM integrity on the association between gut microbiota and NPS in patients with aMCI+. METHODS Twenty patients with aMCI + and 20 healthy controls (HCs) were enrolled. All subjects underwent neuropsychological assessments and their microbial compositions were characterized using 16S rRNA Miseq sequencing technique. Amyloid deposition inspected by positron emission tomography imaging and limbic WM tracts (i.e., fornix, cingulum, and uncinate fasciculus) detected by diffusion tensor imaging were additionally measured in patients with aMCI+. We employed a regression-based mediation analysis using Hayes's PROCESS macro in this study. RESULTS The relative abundance of genera Ruminococcus and Lactococcus was significantly decreased in patients with aMCI + versus HCs. The relative abundance of Ruminococcus was negatively correlated with affective symptom cluster in the aMCI + group. Notably, this association was mediated by WM integrity of the left cingulate gyrus. CONCLUSIONS Our findings suggest Ruminococcus as a potential target for the management of affective impairments in patients with aMCI+.
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Affiliation(s)
- Chun-Che Hung
- Department of Occupational Therapy and Graduate Institute of Behavioral Sciences, Chang Gung University, No. 259, Wenhua 1st Road, 333, Taoyuan, Taiwan
- Laboratory of Brain Imaging and Neural Dynamics (BIND Lab), Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ping Chao
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yejin Lee
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO, USA
| | - Chi-Wei Huang
- Department of Neurology, Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung university College of Medicine, No. 123 Ta-Pei Rd., Niau-Sung Dist, 833, Kaohsiung, Taiwan
| | - Shu-Hua Huang
- Department of Nuclear Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Department of Neurology, Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung university College of Medicine, No. 123 Ta-Pei Rd., Niau-Sung Dist, 833, Kaohsiung, Taiwan.
| | - Chia-Hsiung Cheng
- Department of Occupational Therapy and Graduate Institute of Behavioral Sciences, Chang Gung University, No. 259, Wenhua 1st Road, 333, Taoyuan, Taiwan.
- Laboratory of Brain Imaging and Neural Dynamics (BIND Lab), Chang Gung University, Taoyuan, Taiwan.
- Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan.
- Department of Psychiatry, Chang Gung Memorial Hospital, Linkou, Taiwan.
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5
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Poirier S, Coeuret G, Champomier-Vergès MC, Desmonts MH, Werner D, Feurer C, Frémaux B, Guillou S, Luong NDM, Rué O, Loux V, Zagorec M, Chaillou S. Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios. Front Microbiol 2023; 14:1286661. [PMID: 37920261 PMCID: PMC10619683 DOI: 10.3389/fmicb.2023.1286661] [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: 08/31/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
Background The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics. Methods Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers. Results Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism. Conclusion We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.
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Affiliation(s)
- Simon Poirier
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | - Gwendoline Coeuret
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | | | | | | | | | | | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Valentin Loux
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Stéphane Chaillou
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
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6
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Mahony J, Bottacini F, van Sinderen D. Towards the diversification of lactococcal starter and non-starter species in mesophilic dairy culture systems. Microb Biotechnol 2023; 16:1745-1754. [PMID: 37606352 PMCID: PMC10443329 DOI: 10.1111/1751-7915.14320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 08/23/2023] Open
Abstract
Lactococcus is one of the earliest identified fermentative bacterial genera and among its member species, the dairy-associated Lactococcus lactis and Lactococcus cremoris are undoubtedly the best studied. These two species are believed to have evolved from plant-associated lactococci and through genome decay and acquisition of plasmids, have adapted to the dairy niche. The past decade has witnessed a surge of activity in novel lactococcal species identification from insect, plant and animal sources. Currently, 22 Lactococcus species are described and in this review, we summarise the genome characteristics of and phylogenetic relationships among these species. Furthermore, we explore the role of mobile elements including plasmids and bacteriophages in the diversification of lactococcal species. The pace of identification of novel lactococcal species suggests that the number of lactococcal species is likely to continue to grow. With additional sequence data for the emerging species, it will be possible to perform pathogenicity/virulence risk evaluations and generate extensive insights into the niche adaptation strategies through which they have evolved.
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Affiliation(s)
- Jennifer Mahony
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Francesca Bottacini
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Biological SciencesMunster Technological UniversityCorkIreland
| | - Douwe van Sinderen
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
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Xia J, Jiang N, Zhang B, Sun R, Zhu Y, Xu W, Wang C, Liu Q, Ma Y. Bacterial Changes in Boiled Crayfish between Different Storage Periods and Characterizations of the Specific Spoilage Bacteria. Foods 2023; 12:3006. [PMID: 37628005 PMCID: PMC10453257 DOI: 10.3390/foods12163006] [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: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
This study investigated changes in the microbial compositions of crayfish tails during storage at 4 °C (for 0-12 days) as measured using high-throughput sequencing (HTS). The specific spoilage organisms (SSOs) in the crayfish tails were isolated using culture-dependent cultivation methods, and they were identified by 16S rRNA and characterized for their enzymatic spoilage potentials (e.g., protease, lipase, phospholipase, and amylase). The spoilage abilities of the selected strains in the crayfish tails were assessed by inoculating them into real food. Moreover, the microbial growth and the volatile basic nitrogen (TVB-N) changes were monitored during the storage period. The results from the HTS showed that the dominant genus of shrimp tails evolved from Streptococcus (D0) to Pseudomonas (D4) and, finally, to Paenisporosarcina (D12) during storage. Seven bacterial species (Acinetobacter lwoffii, Aeromonas veronii, Kurthia gibsonii, Pseudomonas sp., Exiguobacterium aurantiacum, Lelliottia amnigena, and Citrobacter freundii) were screened from the spoiled shrimp tails by the culture-dependent method, among which Aeromonas veronii had the strongest spoilage ability.
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Affiliation(s)
- Jiangyue Xia
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China;
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Ning Jiang
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Bin Zhang
- Zhejiang Provincial Key Laboratory of Health Risk Factors for Seafood, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Rongxue Sun
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Yongzhi Zhu
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Weicheng Xu
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Cheng Wang
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Qianyuan Liu
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Yanhong Ma
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (R.S.); (Y.Z.); (W.X.); (C.W.); (Q.L.); (Y.M.)
- Integrated Scientific Research Base for Preservation, Storage and Processing Technology of Aquatic Products of the Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
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Belykh OI, Sorokovikova EG, Tomberg IV, Fedorova GA, Kuzmin AV, Krasnopeev AY, Suslova MY, Potapov SA, Belykh TI, Norovsuren J, Galachyants AD, Tikhonova IV. Water Quality, Toxicity and Diversity of Planktonic and Benthic Cyanobacteria in Pristine Ancient Lake Khubsugul (Hövsgöl), Mongolia. Toxins (Basel) 2023; 15:toxins15030213. [PMID: 36977104 PMCID: PMC10053237 DOI: 10.3390/toxins15030213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
For the first time, microcystin-producing cyanobacteria have been detected in Khubsugul, which is ancient, pristine and one of the world’s largest lakes. The microcystin synthetase genes belonged to the genera Nostoc, Microcystis and possibly Snowella spp. No microcystins were found in the water of the lake. Using the HPLC-HRMS/TOF, five microcystin congeners were identified in biofilms from stony substrates sampled in the coastal zone. The concentration of microcystins in biofilms was low: 41.95 µg g−1 d. wt. by ELISA and 55.8 µg g−1 d. wt. using HPLC. The taxonomic composition of planktonic and benthic cyanobacterial communities was determined by means of microscopy and high-throughput sequencing of 16S rDNA amplicons. Nostocales cyanobacteria dominated benthos of Lake Khubsugul and Synechococcales—plankton. The abundance of cyanobacteria was low both in plankton and benthos; there was no mass development of cyanobacteria. Hydrochemical and microbiological analyses showed that the water in the lake was clean; the number of faecal microorganisms was significantly below the acceptable guideline values. Hydrochemical and hydrophysical parameters, and the concentration of chlorophyll a, were low and within the range of values recorded in the 1970s to 1990s, and corresponded to the oligotrophic state of the lake. There were no signs of anthropogenic eutrophication of the lake and no conditions for the cyanobacterial blooms.
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Affiliation(s)
- Olga I. Belykh
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
- Correspondence: (O.I.B.); (E.G.S.)
| | - Ekaterina G. Sorokovikova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
- Correspondence: (O.I.B.); (E.G.S.)
| | - Irina V. Tomberg
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Galina A. Fedorova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Anton V. Kuzmin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Andrey Yu. Krasnopeev
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Maria Yu. Suslova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Sergey A. Potapov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Tatiana I. Belykh
- Institute for Culture, Social Communication and Information Technology, Baikal State University, 11 Lenin Str., Irkutsk 664003, Russia
| | - Jadambaa Norovsuren
- Institute of Biology of the Mongolian Academy of Sciences, 54B Peace Avenue, Bayanzurkh District, Ulaanbaatar 13330, Mongolia
| | - Agnia D. Galachyants
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Irina V. Tikhonova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
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9
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Microbiological, morpho-textural, and volatile characterization of Portuguese Queijo de Nisa PDO cheese. Food Res Int 2022; 162:112011. [DOI: 10.1016/j.foodres.2022.112011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022]
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10
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Guéneau V, Plateau-Gonthier J, Arnaud L, Piard JC, Castex M, Briandet R. Positive biofilms to guide surface microbial ecology in livestock buildings. Biofilm 2022; 4:100075. [PMID: 35494622 PMCID: PMC9039864 DOI: 10.1016/j.bioflm.2022.100075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 12/12/2022] Open
Abstract
The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.
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11
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Rood L, Bowman JP, Ross T, Corkrey R, Pagnon J, Kaur M, Kocharunchitt C. Spoilage potential of bacterial species from chilled vacuum-packed lamb. Food Microbiol 2022; 107:104093. [DOI: 10.1016/j.fm.2022.104093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/02/2022] [Accepted: 07/12/2022] [Indexed: 11/27/2022]
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12
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Li H, Zhang Y, Yuan X, Liu S, Fan L, Zheng X, Wang S, Yuan L, Jiao X. Microbial biodiversity of raw milk collected from Yangzhou and the heterogeneous biofilm‐forming ability of
Pseudomonas. INT J DAIRY TECHNOL 2022. [DOI: 10.1111/1471-0307.12905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huaxiang Li
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Yanhe Zhang
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Xinhai Yuan
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Siqi Liu
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Luyao Fan
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Xiangfeng Zheng
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Shuo Wang
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Lei Yuan
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu 225127 China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonoses Yangzhou Jiangsu 225009 China
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13
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Manthou E, Coeuret G, Chaillou S, Nychas GJE. Metagenetic characterization of bacterial communities associated with ready-to-eat leafy vegetables and study of temperature effect on their composition during storage. Food Res Int 2022; 158:111563. [DOI: 10.1016/j.foodres.2022.111563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
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14
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Cardinali F, Foligni R, Ferrocino I, Harasym J, Orkusz A, Franciosa I, Milanović V, Garofalo C, Mannozzi C, Mozzon M, Cocolin L, Osimani A, Aquilanti L. Microbial diversity, morpho-textural characterization, and volatilome profile of the Portuguese thistle-curdled cheese Queijo da Beira Baixa PDO. Food Res Int 2022; 157:111481. [DOI: 10.1016/j.foodres.2022.111481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/04/2022]
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15
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Inhibition of Several Bacterial Species Isolated from Squid and Shrimp Skewers by Different Natural Edible Compounds. Foods 2022; 11:foods11050757. [PMID: 35267390 PMCID: PMC8909736 DOI: 10.3390/foods11050757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/10/2022] Open
Abstract
Seafood is an excellent source of nutrients, essential for a healthy diet, ranging from proteins and fatty acids to vitamins and minerals. Seafood products are highly perishable foods due to their nutritional characteristics and composition. The application of nontoxic, natural, and edible preservatives to extend the shelf-life and inhibit bacterial proliferation of several foods has been a hot topic. Consequently, this work aimed to perform the microbiological characterization of squid and shrimp skewers during their shelf-life (five days) and evaluate the susceptibility of randomly isolated microorganisms to several natural edible compounds so that their application for the preservation and shelf-life extension of the product might be analyzed in the future. The product had considerably high total microorganisms loads of about 5 log CFU/g at day zero and 9 log CFU/g at day five. In addition, high bacterial counts of Pseudomonas spp., Enterobacterales, and lactic acid bacteria (LAB) were found, especially on the last day of storage, being Pseudomonas the dominant genus. However, no Escherichia coli or Listeria monocytogenes were detected on the analyzed samples. One hundred bacterial isolates were randomly selected and identified through 16s rRNA sequencing, resulting in the detection of several Enterobacterales, Pseudomonas spp., and LAB. The antibacterial activity of carvacrol, olive leaf extract, limonene, Citrox®, different chitosans, and ethanolic propolis extracts was evaluated by the agar diffusion method, and the minimum inhibitory concentration was determined only for Citrox® since only this solution could inhibit all the identified isolates. At concentrations higher than or equal to 1.69% (v/v), Citrox® demonstrated bacteriostatic and bactericidal activity to 97% and 3% of the isolates, respectively. To our knowledge, there are no available data about the effectiveness of this commercial product on seafood isolates. Although preliminary, this study showed evidence that Citrox® has the potential to be used as a natural preservative in these seafood products, improving food safety and quality while reducing waste. However, further studies are required, such as developing a Citrox®-based coating and its application on this matrix to validate its antimicrobial effect.
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16
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Werum V, Ehrmann M, Vogel R, Hilgarth M. Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat. Microbiol Res 2022; 258:126982. [DOI: 10.1016/j.micres.2022.126982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
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17
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Cheng B, Wen Y, Yang X, Cheng S, Liu L, Chu X, Ye J, Liang C, Yao Y, Jia Y, Zhang F. Gut microbiota is associated with bone mineral density : an observational and genome-wide environmental interaction analysis in the UK Biobank cohort. Bone Joint Res 2021; 10:734-741. [PMID: 34779240 PMCID: PMC8636179 DOI: 10.1302/2046-3758.1011.bjr-2021-0181.r1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIMS Despite the interest in the association of gut microbiota with bone health, limited population-based studies of gut microbiota and bone mineral density (BMD) have been made. Our aim is to explore the possible association between gut microbiota and BMD. METHODS A total of 3,321 independent loci of gut microbiota were used to calculate the individual polygenic risk score (PRS) for 114 gut microbiota-related traits. The individual genotype data were obtained from UK Biobank cohort. Linear regressions were then conducted to evaluate the possible association of gut microbiota with L1-L4 BMD (n = 4,070), total BMD (n = 4,056), and femur total BMD (n = 4,054), respectively. PLINK 2.0 was used to detect the single-nucleotide polymorphism (SNP) × gut microbiota interaction effect on the risks of L1-L4 BMD, total BMD, and femur total BMD, respectively. RESULTS We detected five, three, and seven candidate gut microbiota-related traits for L1-L4 BMD, total BMD, and femur BMD, respectively, such as genus Dialister (p = 0.004) for L1-L4 BMD, and genus Eisenbergiella (p = 0.046) for total BMD. We also detected two common gut microbiota-related traits shared by L1-L4 BMD, total BMD, and femur total BMD, including genus Escherichia Shigella and genus Lactococcus. Interaction analysis of BMD detected several genes that interacted with gut microbiota, such as phospholipase D1 (PLD1) and endomucin (EMCN) interacting with genus Dialister in total BMD, and COL12A1 and Discs Large MAGUK Scaffold Protein 2 (DLG2) interacting with genus Lactococcus in femur BMD. CONCLUSION Our results suggest associations between gut microbiota and BMD, which will be helpful to further explore the regulation mechanism and intervention gut microbiota of BMD. Cite this article: Bone Joint Res 2021;10(11):734-741.
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Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, China
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18
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Wiernasz N, Gigout F, Cardinal M, Cornet J, Rohloff J, Courcoux P, Vigneau E, Skírnisdottír S, Passerini D, Pilet MF, Leroi F. Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products. Foods 2021; 10:foods10112517. [PMID: 34828798 PMCID: PMC8623285 DOI: 10.3390/foods10112517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/02/2023] Open
Abstract
Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This work aimed to compare three products that were obtained from the same batch of fish: cold-smoked salmon (CSS) stored under vacuum packaging (VP) or a modified atmosphere packaging (MAP) and VP salmon dill gravlax (SG). Classical microbiological analyses and 16S rRNA metabarcoding, biochemical analyses (trimethylamine, total volatile basic nitrogen (TVBN), biogenic amines, pH, volatile organic compounds (VOCs)) and sensory analyses (quantitative descriptive analysis) were performed on each product throughout their storage at a chilled temperature. The three products shared the same initial microbiota, which were mainly dominated by Photobacterium, Lactococcus and Lactobacillus genera. On day 28, the VP CSS ecosystem was mainly composed of Photobacterium and, to a lesser extent, Lactococcus and Lactobacillus genera, while Lactobacillus was dominant in the MAP CSS. The diversity was higher in the SG, which was mainly dominated by Enterobacteriaceae, Photobacterium, Lactobacillus and Lactococcus. Although the sensory spoilage was generally weak, gravlax was the most perishable product (slight increase in amine and acidic off-odors and flavors, fatty appearance, slight discoloration and drop in firmness), followed by the VP CSS, while the MAP CSS did not spoil. Spoilage was associated with an increase in the TVBN, biogenic amines and spoilage associated VOCs, such as decanal, nonanal, hexadecanal, benzaldehyde, benzeneacetaldehyde, ethanol, 3-methyl-1-butanol, 2,3-butanediol, 1-octen-3-ol, 2-butanone and 1-octen-3-one. This study showed that the processing and packaging conditions both had an effect on the microbial composition and the quality of the final product.
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Affiliation(s)
- Norman Wiernasz
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
- UMR 1014, Secalim, INRAE, Oniris, 44307 Nantes, France;
| | - Frédérique Gigout
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Mireille Cardinal
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Josiane Cornet
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | - Jens Rohloff
- NTNU, Department of Biology, 7491 Trondheim, Norway;
| | | | | | - Sigurlaug Skírnisdottír
- Matıs, Research and Innovation, Exploitation and Utilization of Genetic Resources, 101-155 Reykjavik, Iceland;
| | - Delphine Passerini
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
| | | | - Françoise Leroi
- IFREMER, BRM, EM3B Laboratory, F-44300 Nantes, France; (N.W.); (F.G.); (M.C.); (J.C.); (D.P.)
- Correspondence:
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19
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Soltani M, Baldisserotto B, Hosseini Shekarabi SP, Shafiei S, Bashiri M. Lactococcosis a Re-Emerging Disease in Aquaculture: Disease Significant and Phytotherapy. Vet Sci 2021; 8:vetsci8090181. [PMID: 34564575 PMCID: PMC8473265 DOI: 10.3390/vetsci8090181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Lactococcosis, particularly that caused by Lactococcus garvieae, is a major re-emerging bacterial disease seriously affecting the sustainability of aquaculture industry. Medicinal herbs and plants do not have very much in vitro antagonism and in vivo disease resistance towards lactococcosis agents in aquaculture. Most in vitro studies with herbal extractives were performed against L. garvieae with no strong antibacterial activity, but essential oils, especially those that contain thymol or carvacrol, are more effective. The differences exhibited by the bacteriostatic and bactericidal functions for a specific extractive in different studies could be due to different bacterial strains or parts of chemotypes of the same plant. Despite essential oils being shown to have the best anti-L. garvieae activity in in vitro assays, the in vivo bioassays required further study. The extracts tested under in vivo conditions presented moderate efficacy, causing a decrease in mortality in infected animals, probably because they improved immune parameters before challenging tests. This review addressed the efficacy of medicinal herbs to lactococcosis and discussed the presented gaps.
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Affiliation(s)
- Mehdi Soltani
- Freshwater Fish Group and Fish Health Unit, Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Department of Aquatic Animal Health, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran;
- Correspondence: or
| | - Bernardo Baldisserotto
- Department of Physiology and Pharmacology, Federal University of Santa Maria, Santa Maria 97105-900, RS, Brazil;
| | | | - Shafigh Shafiei
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord 64165478, Iran;
| | - Masoumeh Bashiri
- Department of Aquatic Animal Health, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran;
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20
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Bahadur A, Zhang W, Sajjad W, Nasir F, Zhang G, Liu G, Chen T. Bacterial diversity patterns of desert dunes in the northeastern Qinghai-Tibet Plateau, China. Arch Microbiol 2021; 203:2809-2823. [PMID: 33730221 DOI: 10.1007/s00203-021-02272-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/02/2023]
Abstract
Limited knowledge about the variation patterns of bacterial community composition in the sand and vegetative ecosystems confines our understanding regarding the contribution of the sand dune to desert areas. In this study, 454 pyrosequencing platforms were adopted to determine the community structure of bacteria and diversity of sand dunes in northeastern Qinghai-Tibet Plateau, China: 50 cm deep, rhizosphere, physical crusts, and biological crusts representing sand and vegetative ecosystems, respectively. The findings revealed significant variation in bacterial diversities and the structure of communities in the sand and vegetative ecosystems. The dominant bacterial phyla of sand and vegetative ecosystems were Firmicutes (47%), Actinobacteria (21%), Proteobacteria (16%), and Bacteroidetes (13%), while Lactococcus (50%) was found to be the dominant genus. Furthermore, samples with high alpha-diversity indices (Chao 1 and Shannon) for the vegetative ecosystem have the lowest modularity index and the largest number of biomarkers, with some exceptions. Redundancy analysis exhibited that environmental factors could explain 72% (phyla) and 67% (genera) of the bacterial communities, with EC, TC, and TOC being the major driving factors. This study expands our understanding of bacterial community composition in the desert ecosystem. The findings suggest that variations in the sand and vegetative ecosystems, such as those predicted by environmental factors, may reduce the abundance and diversity of bacteria, a response that likely affects the provision of key ecosystem processes by desert regions.
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Affiliation(s)
- Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences (CAS), ChangchunJilin Province, 130102, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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21
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Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria. BMC Genomics 2021; 22:28. [PMID: 33413101 PMCID: PMC7788899 DOI: 10.1186/s12864-020-07338-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C. RESULTS We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures. CONCLUSIONS The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.
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22
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Hilgarth M, Werum V, Vogel RF. Lactococcus carnosus sp. nov. and Lactococcus paracarnosus sp. nov., two novel species isolated from modified-atmosphere packaged beef steaks. Int J Syst Evol Microbiol 2020; 70:5832-5840. [DOI: 10.1099/ijsem.0.004481] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As part of a study investigating the spoilage microbiome of modified-atmosphere packaged beef from Germany, four novel strains of lactic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they could not be assigned to known species. The isolates were Gram-staining-positive, coccoid, facultatively anaerobic, non-motile, catalase-negative and oxidase-negative. Morphological, physiological and phylogenetic analysis revealed a distinct lineage within the genus
Lactococcus
, with
Lactococcus piscium
and
Lactococcus plantarum
as closest relatives. Results indicated that they represented two different novel species with two strains, (TMW 2.1612T/TMW 2.1613 and TMW 2.1615T/TMW 2.1614), respectively. The two strains of both novel species shared identical 16S rRNA gene sequences but a MLSA allowed their intraspecies differentiation. The 16S rRNA gene sequences of TMW 2.1612T and TMW 2.1615T had a similarity of 99.85 % to each other and a similarity of 99.85 and 99.78 % the most closely related type strain of
Lactococcus piscium
, respectively. However, the ANIb value between the respective type strains TMW 2.1612T and TMW 2.1615T, and the type strain of
Lactococcus piscium
was only 94.3 and 92.0 %, respectively, and 92.9 % between TMW 2.1612T and TMW 2.1615T. The in silico DDH estimate value between the respective type strain TMW 2.1612T and TMW 2.1615T and the most closely related type strain of
Lactococcus piscium
was only 59.9 and 48.9 %, respectively, and 51.1 % between TMW 2.1612T and TMW 2.1615T. Peptidoglycan type of strain TMW 2.1612T is Lys–Thr–Ala and major fatty acids are summed feature 8 and C16 : 0. Peptidoglycan type of strain TMW 2.1615T is Lys–Ala and major fatty acids are C16 : 0, C19 : 0cyclo ω8c and summed feature 8. On the basis of polyphasic evidence, the meat isolates represent two novel species of the genus
Lactococcus
, for which the names Lactococcus carnosus sp. nov and Lactococcus paracarnosus sp. nov are proposed. The designated respective type strains are TMW 2.1612T (=DSM 111016T =CECT 30115T) and TWM 2.1615T (=DSM 111017T =CECT 30116T).
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Affiliation(s)
- Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Victoria Werum
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
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An evaluation of the core bacterial communities associated with hypersaline environments in the Qaidam Basin, China. Arch Microbiol 2020; 202:2093-2103. [PMID: 32488562 DOI: 10.1007/s00203-020-01927-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022]
Abstract
Hypersaline lakes and saltern areas are important industrial and biodiversity resources in the Qaidam Basin of China that reside at > 2600 m asl. Most hypersaline environments in this area are characterized by saturated salinity (~ 300 g/L salinity), nearly neutral pH, intense ultraviolet radiation, and extremely variable temperature fluctuations. The core bacterial communities associated with these stressful environments have nevertheless remained uninvestigated. 16S rRNA gene Illumina sequencing analyses revealed that the bacterial communities were dominated by core lineages including the Proteobacteria (39.4-64.6%) and the Firmicutes (17.0-42.7%). However, the relative abundances of common lineages, and especially the five most abundant taxa of Pseudomonas, Lactococcus, Anoxybacillus, Acinetobacter, and Brevundimonas, were highly variable across communities and closely associated with hypersaline characteristics in the samples. Network analysis revealed the presence of co-occurrence high relative abundance taxa (cluster I) that were highly correlated across all hypersaline samples. Additionally, temperature, total organic carbon, K+, and Mg2+ correlated highest with taxonomic distributions across communities. These results highlight the potential mechanisms that could underlie survival and adaptation to these extreme hypersaline ecosystems.
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24
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Wiernasz N, Leroi F, Chevalier F, Cornet J, Cardinal M, Rohloff J, Passerini D, Skırnisdóttir S, Pilet MF. Salmon Gravlax Biopreservation With Lactic Acid Bacteria: A Polyphasic Approach to Assessing the Impact on Organoleptic Properties, Microbial Ecosystem and Volatilome Composition. Front Microbiol 2020; 10:3103. [PMID: 32038547 PMCID: PMC6986196 DOI: 10.3389/fmicb.2019.03103] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/23/2019] [Indexed: 11/16/2022] Open
Abstract
Seafood and fishery products are very perishable commodities with short shelf-lives owing to rapid deterioration of their organoleptic and microbiological quality. Microbial growth and activity are responsible for up to 25% of food losses in the fishery industry. In this context and to meet consumer demand for minimally processed food, developing mild preservation technologies such as biopreservation represents a major challenge. In this work, we studied the use of six lactic acid bacteria (LAB), previously selected for their properties as bioprotective agents, for salmon dill gravlax biopreservation. Naturally contaminated salmon dill gravlax slices, with a commercial shelf-life of 21 days, were purchased from a French industrial company and inoculated by spraying with the protective cultures (PCs) to reach an initial concentration of 106 log CFU/g. PC impact on gravlax microbial ecosystem (cultural and acultural methods), sensory properties (sensory profiling test), biochemical parameters (pH, TMA, TVBN, biogenic amines) and volatilome was followed for 25 days of storage at 8°C in vacuum packaging. PC antimicrobial activity was also assessed in situ against Listeria monocytogenes. This polyphasic approach underlined two scenarios depending on the protective strain. Carnobacterium maltaromaticum SF1944, Lactococcus piscium EU2229 and Leuconostoc gelidum EU2249, were very competitive in the product, dominated the microbial ecosystem, and displayed antimicrobial activity against the spoilage microbiota and L. monocytogenes. The strains also expressed their own sensory and volatilome signatures. However, of these three strains, C. maltaromaticum SF1944 did not induce strong spoilage and was the most efficient for L. monocytogenes growth control. By contrast, Vagococcus fluvialis CD264, Carnobacterium inhibens MIP2551 and Aerococcus viridans SF1044 were not competitive, did not express strong antimicrobial activity and produced only few organic volatile compounds (VOCs). However, V. fluvialis CD264 was the only strain to extend the sensory quality, even beyond 25 days. This study shows that C. maltaromaticum SF1944 and V. fluvialis CD264 both have a promising potential as bioprotective cultures to ensure salmon gravlax microbial safety and sensorial quality, respectively.
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Affiliation(s)
- Norman Wiernasz
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B), Ifremer, Nantes, France
- UMR 1014 SECALIM, INRA, Oniris, Nantes, France
| | - Françoise Leroi
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B), Ifremer, Nantes, France
| | - Frédérique Chevalier
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B), Ifremer, Nantes, France
| | - Josiane Cornet
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B), Ifremer, Nantes, France
| | - Mireille Cardinal
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B), Ifremer, Nantes, France
| | - Jens Rohloff
- NTNU, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Delphine Passerini
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B), Ifremer, Nantes, France
| | - Sigurlaug Skırnisdóttir
- Matıs, Research and Innovation, Exploitation and Utilization of Genetic Resources, Reykjavik, Iceland
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25
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Leneveu-Jenvrin C, Charles F, Barba FJ, Remize F. Role of biological control agents and physical treatments in maintaining the quality of fresh and minimally-processed fruit and vegetables. Crit Rev Food Sci Nutr 2019; 60:2837-2855. [PMID: 31547681 DOI: 10.1080/10408398.2019.1664979] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fruit and vegetables are an important part of human diets and provide multiple health benefits. However, due to the short shelf-life of fresh and minimally-processed fruit and vegetables, significant losses occur throughout the food distribution chain. Shelf-life extension requires preserving both the quality and safety of food products. The quality of fruit and vegetables, either fresh or fresh-cut, depends on many factors and can be determined by analytical or sensory evaluation methods. Among the various technologies used to maintain the quality and increase shelf-life of fresh and minimally-processed fruit and vegetables, biological control is a promising approach. Biological control refers to postharvest control of pathogens using microbial cultures. With respect to application of biological control for increasing the shelf-life of food, the term biopreservation is favored, although the approach is identical. The methods for screening and development of biocontrol agents differ greatly according to their intended application, but the efficacy of all current approaches following scale-up to commercial conditions is recognized as insufficient. The combination of biological and physical methods to maintain quality has the potential to overcome the limitations of current approaches. This review compares biocontrol and biopreservation approaches, alone and in combination with physical methods. The recent increase in the use of meta-omics approaches and other innovative technologies, has led to the emergence of new strategies to increase the shelf-life of fruit and vegetables, which are also discussed herein.
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Affiliation(s)
- Charlène Leneveu-Jenvrin
- QualiSud, Université de La Réunion, CIRAD, Université Montpellier, Montpellier SupAgro, Université d'Avignon, Sainte Clotilde, France
| | - Florence Charles
- QualiSud, Université d'Avignon, CIRAD, Université Montpellier, Montpellier SupAgro, Université de La Réunion, Avignon, France
| | - Francisco J Barba
- Faculty of Pharmacy, Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Burjassot, València, Spain
| | - Fabienne Remize
- QualiSud, Université de La Réunion, CIRAD, Université Montpellier, Montpellier SupAgro, Université d'Avignon, Sainte Clotilde, France
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26
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Rapid detection and control of psychrotrophic microorganisms in cold storage foods: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Zhang J, Li Y, Liu X, Lei Y, Regenstein JM, Luo Y. Characterization of the microbial composition and quality of lightly salted grass carp (Ctenopharyngodon idellus) fillets with vacuum or modified atmosphere packaging. Int J Food Microbiol 2019; 293:87-93. [DOI: 10.1016/j.ijfoodmicro.2018.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 12/13/2018] [Accepted: 12/22/2018] [Indexed: 12/25/2022]
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28
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Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis, Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas lundensis, and Weissella viridescens, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage. GENOME ANNOUNCEMENTS 2018; 6:6/24/e00479-18. [PMID: 29903812 PMCID: PMC6003748 DOI: 10.1128/genomea.00479-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, we present the draft genome sequences of nine strains from various psychrotrophic species identified in meat products and being recognized as important emerging food spoilers. Many of these species have only one or few strains being sequenced, and this work will contribute to the improvement of the overall genomic knowledge about them.
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29
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Pan Z, Li L, Shen Z, Chen Y, Li M. Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing. J Food Prot 2018; 81:1022-1029. [PMID: 29761724 DOI: 10.4315/0362-028x.jfp-17-498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The microbial communities in air- and vacuum-packed crisp grass carp ( Ctenopharyngodon idella C. et V.) fillets have not been characterized during chilled storage. High-throughput sequencing of bacterial 16S rRNA has now revealed that the bacterial community in fresh fillets is diverse and distinct from that in spoiled samples. The predominant phylum was Proteobacteria, and 66 genera were identified. In fresh fillets, the most abundant genera were Acinetobacter (53.3%), Wautersiella (6.3%), unclassified Alcaligenaceae (4.4%), Stenotrophomonas (3.8%), unclassified Enterobacteriaceae (3.8%), and Enhydrobacter (3.6%). These genera diminished during chilled storage and sometimes disappeared. At the end of storage, Aeromonas and Pseudomonas were the most abundant. Similar results were obtained by PCR-denaturing gradient gel electrophoresis. These data provide detailed insight into the evolving bacterial communities in air- and vacuum-packed crisp grass carp fillets during storage, revealing Aeromonas and Pseudomonas as major spoilage organisms. These data may be useful for improvement of crisp grass carp quality and shelf life during chilled storage.
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Affiliation(s)
- Ziqiang Pan
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Lin Li
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Zhihua Shen
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Yan Chen
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
| | - Mei Li
- College of Chemistry and Biology, Zhongshan Institute, University of Electronic Science and Technology of China, Zhongshan 528402, People's Republic of China
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30
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Chaix E, Deléger L, Bossy R, Nédellec C. Text mining tools for extracting information about microbial biodiversity in food. Food Microbiol 2018; 81:63-75. [PMID: 30910089 PMCID: PMC6460834 DOI: 10.1016/j.fm.2018.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/26/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022]
Abstract
Information on food microbial diversity is scattered across millions of scientific papers. Researchers need tools to assist their bibliographic search in such large collections. Text mining and knowledge engineering methods are useful to automatically and efficiently find relevant information in Life Science. This work describes how the Alvis text mining platform has been applied to a large collection of PubMed abstracts of scientific papers in the food microbiology domain. The information targeted by our work is microorganisms, their habitats and phenotypes. Two knowledge resources, the NCBI taxonomy and the OntoBiotope ontology were used to detect this information in texts. The result of the text mining process was indexed and is presented through the AlvisIR Food on-line semantic search engine. In this paper, we also show through two illustrative examples the great potential of this new tool to assist in studies on ecological diversity and the origin of microbial presence in food. We present new text-mining tools to extract information in food microbiology. The results of the extraction are available in an on-line semantic search engine. Taxa, habitats, phenotypes and links between them can be queried in PubMed abstracts. Text-mining tools could assist to browse past and recent scientific literature. Two use-cases are presented: fruit microbiota and spore-forming bacteria in food.
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Affiliation(s)
- Estelle Chaix
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Louise Deléger
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Robert Bossy
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Claire Nédellec
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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31
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Hilgarth M, Nani M, Vogel R. Assertiveness of meat‐borne
Lactococcus piscium
strains and their potential for competitive exclusion of spoilage bacteria
in situ
and
in vitro. J Appl Microbiol 2018; 124:1243-1253. [DOI: 10.1111/jam.13710] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/09/2018] [Accepted: 01/22/2018] [Indexed: 11/29/2022]
Affiliation(s)
- M. Hilgarth
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - M. Nani
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - R.F. Vogel
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
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32
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Silbande A, Cornet J, Cardinal M, Chevalier F, Rochefort K, Smith-Ravin J, Adenet S, Leroi F. Characterization of the spoilage potential of pure and mixed cultures of bacterial species isolated from tropical yellowfin tuna (Thunnus albacares). J Appl Microbiol 2018; 124:559-571. [DOI: 10.1111/jam.13663] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 12/01/2017] [Indexed: 11/28/2022]
Affiliation(s)
- A. Silbande
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B); Ifremer; Nantes France
- Pôle Agroalimentaire Régional de Martinique (PARM); Ifremer; Lamentin Martinique
- Département Scientifique Inter facultaire (DSI); EA929 AIHP-GEODE (groupe BIOSPHERES); Université des Antilles; Schœlcher Martinique
| | - J. Cornet
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B); Ifremer; Nantes France
| | - M. Cardinal
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B); Ifremer; Nantes France
| | - F. Chevalier
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B); Ifremer; Nantes France
| | - K. Rochefort
- Pôle Agroalimentaire Régional de Martinique (PARM); Ifremer; Lamentin Martinique
| | - J. Smith-Ravin
- Département Scientifique Inter facultaire (DSI); EA929 AIHP-GEODE (groupe BIOSPHERES); Université des Antilles; Schœlcher Martinique
| | - S. Adenet
- Pôle Agroalimentaire Régional de Martinique (PARM); Ifremer; Lamentin Martinique
| | - F. Leroi
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM3B); Ifremer; Nantes France
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33
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Han R, Zhang X, Liu J, Long Q, Chen L, Liu D, Zhu D. Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 2017; 63:895-908. [PMID: 28850799 DOI: 10.1139/cjm-2016-0773] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl-, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.
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Affiliation(s)
- Rui Han
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.,b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Xin Zhang
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Jing Liu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Qifu Long
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Laisheng Chen
- b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Deli Liu
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Derui Zhu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
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34
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Isolation of two lactobacilli, producers of two new bacteriocin-like substances (BLS) for potential food-preservative use. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2913-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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