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Choi GH, Fugaban JII, Dioso CM, Bucheli JEV, Holzapfel WH, Todorov SD. Antimicrobial Peptides (Bacteriocins) Produced by Lactococcus lactis and Pediococcus pentosaceus Strains with Activity Against Clinical and Food-Borne Pathogens. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10188-x. [PMID: 38038837 DOI: 10.1007/s12602-023-10188-x] [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] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Bacteriocins are ribosomal-synthesized peptides with antimicrobial activity, produced by different groups of bacteria, including lactic acid bacteria (LAB). Most of the produced by LAB bacteriocins can be described with rather broad spectra of inhibition and they offer suggested applications in food preservation and pharmaceutical sector. Different LAB were isolated from fermented food products and fruits, obtained from the region of Pohang, Korea, and identified based on physiological, biochemical, and molecular methods. The promising isolates, Pediococcus pentosaceus 732, Lactococcus lactis 808, and Lactococcus lactis subsp. lactis 431, were identified based on biochemical, physiological, and biomolecular approaches, including 16S rRNA partial sequencing, and were evaluated for production of bacteriocin, including stability in presence of enzymes, chemicals, pH, and temperatures. Adherence properties for the expressed bacteriocins by P. pentosaceus 732, Lc. lactis 808, and Lc. lactis subsp. lactis 431 were evaluated at presence of selected chemicals, pH, and temperatures. The presence of bacteriocin genes in the strains was investigated and analyzed. The bacterial effect of bacteriocin produced by studied strains on Listeria spp. and Staphylococcus spp. has been shown for actively growing and stationary cells. Similar growth and bacteriocin production were observed when studied strains were cultured in MRS at 30 °C or 37 °C. The presence of nisin operon with some point mutations on the genomic DNA was recorded based on the performed PCR reactions targeting different genes associated with nisin expression for both lactococcal strains. Pediocin PA-1 operon was evaluated in a similar manner for P. pentosaceus 732.
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Affiliation(s)
- Gee Hyeun Choi
- ProBacLab, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea
| | - Joanna Ivy Irorita Fugaban
- ProBacLab, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark
| | - Clarizza May Dioso
- HEM Laboratory, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea
- Department of Molecular Biotechnology, Environmental Technology and Food Technology, Ghent University Global Campus, 119, Songdomunhawa-Ro, Yeonsu-Gu, Incheon, 21985, South Korea
| | - Jorge Enrique Vazquez Bucheli
- ProBacLab, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea
- HEM Laboratory, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea
| | - Wilhelm Heinrich Holzapfel
- HEM Laboratory, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea
| | - Svetoslav Dimitrov Todorov
- ProBacLab, Department of Advanced Convergence, Handong Global University, 37554, Pohang, Gyeongbuk, Republic of Korea.
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana Do Castelo, 4900-347, Viana Do Castelo, Portugal.
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2
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [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] [Indexed: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Pinar-Méndez A, Galofré B, Blanch AR, García-Aljaro C. Culture and molecular methods as complementary tools for water quality management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157789. [PMID: 35931155 DOI: 10.1016/j.scitotenv.2022.157789] [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: 07/05/2022] [Revised: 07/30/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Bacterial communities in a full-scale drinking water treatment plant (DWTP) were characterized using matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) to identify HPC isolates and the obtained results were compared to 16S rRNA (V4) metabarcoding data acquired in a previous study. Sixty-three samples were collected at nine stages of the potabilization process: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, the mixing chamber and post-chlorination drinking water. In total, 1807 bacterial colonies were isolated, 32 % of which were successfully identified to at least the genus level by MALDI-TOF MS using our previously developed Drinking Water Library. Trends in diversity were similar by both approaches, but differences were observed in the detection of taxa, especially at lower hierarchy levels. High bacterial diversity was observed in river and groundwater, where Proteobacteria predominated. The diversity decreased significantly after the chlorination step, where Bacillus sp. (Firmicutes) and an unknown genus of Obscuribacteraceae (Cyanobacteria) were the most prevalent genera according to MALDI-TOF MS and metabarcoding, respectively. The two approaches gave similar results for the decantation, sand filtration and mixing chamber steps, where the most abundant taxon was Flavobacterium. The combined use of these culture-based and culture-independent methods to characterize microbial populations may help to better understand the role of bacteria in water treatment and quality, which will be of value for DWTP management.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | - Cristina García-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
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Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [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: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
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Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
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Paquin P, Durmort C, Paulus C, Vernet T, Marcoux PR, Morales S. Spatio-temporal based deep learning for rapid detection and identification of bacterial colonies through lens-free microscopy time-lapses. PLOS DIGITAL HEALTH 2022; 1:e0000122. [PMID: 36812631 PMCID: PMC9931332 DOI: 10.1371/journal.pdig.0000122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 09/09/2022] [Indexed: 06/18/2023]
Abstract
Detection and identification of pathogenic bacteria isolated from biological samples (blood, urine, sputum, etc.) are crucial steps in accelerated clinical diagnosis. However, accurate and rapid identification remain difficult to achieve due to the challenge of having to analyse complex and large samples. Current solutions (mass spectrometry, automated biochemical testing, etc.) propose a trade-off between time and accuracy, achieving satisfactory results at the expense of time-consuming processes, which can also be intrusive, destructive and costly. Moreover, those techniques tend to require an overnight subculture on solid agar medium delaying bacteria identification by 12-48 hours, thus preventing rapid prescription of appropriate treatment as it hinders antibiotic susceptibility testing. In this study, lens-free imaging is presented as a possible solution to achieve a quick and accurate wide range, non-destructive, label-free pathogenic bacteria detection and identification in real-time using micro colonies (10-500 μm) kinetic growth pattern combined with a two-stage deep learning architecture. Bacterial colonies growth time-lapses were acquired thanks to a live-cell lens-free imaging system and a thin-layer agar media made of 20 μl BHI (Brain Heart Infusion) to train our deep learning networks. Our architecture proposal achieved interesting results on a dataset constituted of seven different pathogenic bacteria-Staphylococcus aureus (S. aureus), Enterococcus faecium (E. faecium), Enterococcus faecalis (E. faecalis), Staphylococcus epidermidis (S. epidermidis), Streptococcus pneumoniae R6 (S. pneumoniae), Streptococcus pyogenes (S. pyogenes), Lactococcus Lactis (L. Lactis). At T = 8h, our detection network reached an average 96.0% detection rate while our classification network precision and sensitivity averaged around 93.1% and 94.0% respectively, both were tested on 1908 colonies. Our classification network even obtained a perfect score for E. faecalis (60 colonies) and very high score for S. epidermidis at 99.7% (647 colonies). Our method achieved those results thanks to a novel technique coupling convolutional and recurrent neural networks together to extract spatio-temporal patterns from unreconstructed lens-free microscopy time-lapses.
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Affiliation(s)
- Paul Paquin
- Univ. Grenoble Alpes, CEA, LETI, DTBS, LSIV, 38054 Grenoble, France
| | - Claire Durmort
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38054 Grenoble, France
| | - Caroline Paulus
- Univ. Grenoble Alpes, CEA, LETI, DTBS, LSIV, 38054 Grenoble, France
| | - Thierry Vernet
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38054 Grenoble, France
| | | | - Sophie Morales
- Univ. Grenoble Alpes, CEA, LETI, DTBS, LSIV, 38054 Grenoble, France
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Nnachi RC, Sui N, Ke B, Luo Z, Bhalla N, He D, Yang Z. Biosensors for rapid detection of bacterial pathogens in water, food and environment. ENVIRONMENT INTERNATIONAL 2022; 166:107357. [PMID: 35777116 DOI: 10.1016/j.envint.2022.107357] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.
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Affiliation(s)
- Raphael Chukwuka Nnachi
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Bowen Ke
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 61004, PR China
| | - Zhenhua Luo
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom; Healthcare Technology Hub, Ulster University, Jordanstown Shore Road, BT37 0QB, Northern Ireland, United Kingdom
| | - Daping He
- School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom.
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Zawistowska-Rojek A, Zaręba T, Tyski S. Microbiological Testing of Probiotic Preparations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095701. [PMID: 35565098 PMCID: PMC9099753 DOI: 10.3390/ijerph19095701] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023]
Abstract
Probiotic microorganisms that are potentially beneficial to the health of the host are commercially available in a great variety of products. Not all microorganism strains present in products have proven beneficial to the health properties. These products include not only foodstuffs but also dietary supplements, food for special medical purposes, medicinal products, as well as cosmetics and medical devices. These products contain from one to a dozen bacterial strains of the same or different species and sometimes also fungal strains. Since the pro-health effects of probiotics depend on a specific strain, the number of its cells in a dose, and the lack of pathogenic microorganisms, it is extremely important to control the quality of probiotics. Depending on the classification of a given product, its form, and its content of microorganisms, the correct determination of the number of microorganisms and their identification is crucial. This article describes the culture-dependent and culture-independent methods for testing the contents of probiotic microorganisms, in addition to biochemical and genetic methods of identification. The microbiological purity requirements for various product categories are also presented. Due to numerous reports on the low quality of probiotic products available on the market, it is important to standardise research methods for this group of products and to increase the frequency of inspections of these products.
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Affiliation(s)
- Anna Zawistowska-Rojek
- Department of Antibiotics and Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (T.Z.); (S.T.)
- Department of Pharmaceutical Microbiology, Medical University of Warsaw, Banacha 1b, 02-097 Warsaw, Poland
- Correspondence:
| | - Tomasz Zaręba
- Department of Antibiotics and Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (T.Z.); (S.T.)
| | - Stefan Tyski
- Department of Antibiotics and Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (T.Z.); (S.T.)
- Department of Pharmaceutical Microbiology, Medical University of Warsaw, Banacha 1b, 02-097 Warsaw, Poland
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8
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Characterization and Viability Prediction of Commercial Probiotic Supplements under Temperature and Concentration Conditioning Factors by NIR Spectroscopy. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8020066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The quality of probiotics has been associated with bacteria and yeast strains’ contents and their stability against conditioning factors. Near-infrared spectroscopy (NIRS), as a non-destructive, fast, real-time, and cost-effective analytical technique, can provide some advantages over more traditional food quality control methods in quality evaluation. The aim of our study was to evaluate the applicability of NIRS to the characterization and viability prediction of three commercial probiotic food supplement powders containing lactic acid bacteria (LAB) subjected to concentration and temperature conditioning factors. For each probiotic, 3 different concentrations were considered, and besides normal preparation (25 °C, control), samples were subjected to heat treatment at 60 or 90 °C and left to cool down until reaching room temperature prior to further analysis. Overall, after applying chemometrics to the NIR spectra, the obtained principal component analysis-based linear discriminant analysis (PCA-LDA) classification models showed a high accuracy in both recognition and prediction. The temperature has an important impact on the discrimination of samples. According to the concentration, the best models were identified for the 90 °C temperature treatment, reaching 100% average correct classification for recognition and over 90% for prediction. However, the prediction accuracy decreased substantially at lower temperatures. For the 25°C temperature treatment, the prediction accuracy decreased to nearly 60% for 2 of the 3 probiotics. Moreover, according to the temperature level, both the recognition and prediction accuracies were close to 100%. Additionally, the partial least square regression (PLSR) model achieved respectable values for the prediction of the colony-forming units (log CFU/g) of the probiotic samples, with a determination coefficient for prediction (R2Pr) of 0.82 and root mean square error for prediction (RMSEP) of 0.64. The results of our study show that NIRS is a fast, reliable, and promising alternative to the conventional microbiology technique for the characterization and prediction of the viability of probiotic supplement drink preparations.
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HU Q, ZHAO J, LUO R, YOU L, ZHAO X, SU C, ZHANG H. The influence of microbial bacterial proteins on metabolites in the chilled tan sheep meat. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.24822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Mazzantini D, Celandroni F, Calvigioni M, Panattoni A, Labella R, Ghelardi E. Microbiological Quality and Resistance to an Artificial Gut Environment of Two Probiotic Formulations. Foods 2021; 10:foods10112781. [PMID: 34829062 PMCID: PMC8617924 DOI: 10.3390/foods10112781] [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: 09/29/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/18/2022] Open
Abstract
The quality control of probiotic products is the focus of numerous organizations worldwide. Several studies have highlighted the poor microbiological quality of many commercial probiotic formulations in terms of the identity of the contained microorganisms, viability, and purity, thus precluding the expected health benefits and representing a potential health risk for consumers. In this paper, we analyzed the contents of two probiotic formulations, one composed of an encapsulated mixture of lactobacilli and bifidobacteria, and one by a lyophilized yeast. The microorganisms contained in the products were quantified and identified using up-to-date methodologies, such as MALDI-TOF MS and metagenomic analysis. Moreover, as acid and bile tolerance is included among the criteria used to select probiotic microorganisms, in vitro tests were performed to evaluate the behavior of the formulations in conditions mimicking the harsh gastric environment and the intestinal fluids. Our results indicate the high quality of the formulations in terms of the enumeration and identification of the contained organisms, as well as the absence of contaminants. Moreover, both products tolerated the acidic conditions well, with encapsulation providing further protection for the microorganisms. A good tolerance to the simulated artificial intestinal conditions was also evidenced for both preparations.
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Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy; (D.M.); (F.C.); (M.C.); (A.P.)
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy; (D.M.); (F.C.); (M.C.); (A.P.)
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy; (D.M.); (F.C.); (M.C.); (A.P.)
| | - Adelaide Panattoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy; (D.M.); (F.C.); (M.C.); (A.P.)
| | - Roberto Labella
- Sanofi Consumer Health Care, Reading, Berkshire RG6 1PT, UK;
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy; (D.M.); (F.C.); (M.C.); (A.P.)
- Research Center Nutraceuticals and Food for Health-Nutrafood, University of Pisa, 56127 Pisa, Italy
- Correspondence: ; Tel.: +39-050-221-3679
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Pinar-Méndez A, Fernández S, Baquero D, Vilaró C, Galofré B, González S, Rodrigo-Torres L, Arahal DR, Macián MC, Ruvira MA, Aznar R, Caudet-Segarra L, Sala-Comorera L, Lucena F, Blanch AR, Garcia-Aljaro C. Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database. WATER RESEARCH 2021; 203:117543. [PMID: 34433109 DOI: 10.1016/j.watres.2021.117543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/23/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain; Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
| | - Sonia Fernández
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - David Baquero
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Carles Vilaró
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Susana González
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - M Carmen Macián
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Rosa Aznar
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Laia Caudet-Segarra
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Francisco Lucena
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
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12
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Mazzantini D, Calvigioni M, Celandroni F, Lupetti A, Ghelardi E. Spotlight on the Compositional Quality of Probiotic Formulations Marketed Worldwide. Front Microbiol 2021; 12:693973. [PMID: 34354690 PMCID: PMC8329331 DOI: 10.3389/fmicb.2021.693973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
On the worldwide market, a great number of probiotic formulations are available to consumers as drugs, dietary supplements, and functional foods. For exerting their beneficial effects on host health, these preparations should contain a sufficient amount of the indicated living microbes and be pathogen-free to be safe. Therefore, the contained microbial species and their amount until product expiry are required to be accurately reported on the labels. While commercial formulations licensed as drugs are subjected to rigorous quality controls, less stringent regulations are generally applied to preparations categorized as dietary supplements and functional foods. Many reports indicated that the content of several probiotic formulations does not always correspond to the label claims in terms of microbial identification, number of living organisms, and purity, highlighting the requirement for more stringent quality controls by manufacturers. The main focus of this review is to provide an in-depth overview of the microbiological quality of probiotic formulations commercialized worldwide. Many incongruences in the compositional quality of some probiotic formulations available on the worldwide market were highlighted. Even if manufacturers carry at least some of the responsibility for these inconsistencies, studies that analyze probiotic products should be conducted following recommended and up-to-date methodologies.
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Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.,Research Center Nutraceuticals and Food for Health-Nutrafood, University of Pisa, Pisa, Italy
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13
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Mohar Lorbeg P, Golob M, Kramer M, Treven P, Bogovič Matijašić B. Evaluation of Dietary Supplements Containing Viable Bacteria by Cultivation/MALDI-TOF Mass Spectrometry and PCR Identification. Front Microbiol 2021; 12:700138. [PMID: 34349743 PMCID: PMC8326757 DOI: 10.3389/fmicb.2021.700138] [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: 04/25/2021] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
The insufficient quality of products containing beneficial live bacteria in terms of content and viability of labelled microorganisms is an often-reported problem. The aim of this work was to evaluate the quality of dietary supplements containing viable bacteria available in Slovenian pharmacies using plate counting, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and species- or subspecies-specific PCR with DNA isolated from consortia of viable bacteria, from individual isolates, or directly from the products. Twelve percent of the products (3 of 26) contained insufficient numbers of viable bacteria. Eighty-three of the labelled species (111 in total) were confirmed by PCR with DNA from the product; 74% of these were confirmed by PCR with DNA from viable consortium, and 65% of these were confirmed by MALDI-TOF MS analysis of colonies. Certain species in multi-strain products were confirmed by PCR with DNA from viable consortia but not by MALDI-TOF MS, suggesting that the number of isolates examined (three per labelled strain) was too low. With the exception of Lacticaseibacillus casei and closely related species (Lacticaseibacillus rhamnosus and Lacticaseibacillus zeae), PCR and MALDI-TOF identification results agreed for 99% of the isolates examined, although several MALDI-TOF results had lower score values (1.700-1.999), indicating that the species identification was not reliable. The species L. zeae, which appeared in 20 matches of the Biotyper analysis, was identified as L. rhamnosus by PCR. The MALDI-TOF MS analysis was also unsuccessful in detecting Lactobacillus acidophilus La-5 and Bacillus coagulans due to missing peaks and unreliable identification, respectively. Mislabelling was detected by both methods for two putative L. casei strains that turned out to belong to the species Lacticaseibacillus paracasei. PCR remains more successful in subspecies-level identification as long as the database of MALDI-TOF MS spectra is not expanded by building in-house databases. The lack of positive PCR results with viable consortia or colonies, but positive PCR results with DNA isolated directly from the products observed in 10% (11/112) of the labelled strains, suggests the presence of non-culturable bacteria in the products. MALDI-TOF MS is a faster and simpler alternative to PCR identification, provided that a sufficient number of colonies are examined. Generation of in-house library may further improve the identification accuracy at the species and sub-species level.
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Affiliation(s)
- Petra Mohar Lorbeg
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
| | - Majda Golob
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Kramer
- Global Drug Development, Technical Research & Development, Biologics and Cell & Gene Therapy, Novartis, Global Project Management Office, Lek Pharmaceuticals d.d., Mengeš, Slovenia
| | - Primož Treven
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
| | - Bojana Bogovič Matijašić
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
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14
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Rodrigues NPA, Garcia EF, de Souza EL. Selection of lactic acid bacteria with promising probiotic aptitudes from fruit and ability to survive in different food matrices. Braz J Microbiol 2021; 52:2257-2269. [PMID: 34125419 DOI: 10.1007/s42770-021-00543-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/08/2021] [Indexed: 11/29/2022] Open
Abstract
Lactic acid bacteria (LAB) are among the most prevalent microorganisms forming the autochthonous microbiota of fruit. This study aimed to select LAB isolates with probiotic aptitudes from apple, banana, grape, and orange through evaluation of in vitro safety, technological, and functional-related properties. The ability of most promising selected isolates to survive in commercial apple and orange juice, meat stew, vegetable puree, and UHT milk during 28 days of refrigeration storage was evaluated. Ninety-three isolates identified preliminarily as LAB were recovered from fruit and 66 of these isolates passed safety tests. Most of these isolates were pre-identified as belonging to Lactobacillus or Enterococcus genus based on MALDI-ToF MS profiling. These 66 isolates were categorized into three homogeneous groups based on a preliminary cluster analysis run with data from experiments to measure technological characteristics. Nine LAB isolates were selected as the most promising for probiotic use based on a principal component analysis run with data from experiments to measure probiotic-related properties. Four of these isolates were sensitive to different antibiotics and identified (16S-rRNA gene sequencing) as Lactobacillus brevis (recently reclassified as L. brevis) or Lactobacillus spp. These 4 selected isolates had high viable counts and high percentages of physiologically active cells in apple and orange juice, beef stew, vegetable puree, and UHT milk during refrigeration storage. The results showed that apple, banana, orange, and grape are potential sources of LAB with aptitudes to be exploited for a possible probiotic use and distinguished abilities to survive in different food matrices.
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Affiliation(s)
- Noádia Priscilla Araújo Rodrigues
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I, João Pessoa, Paraíba, Brazil.,Departamento de Gastronomia, Centro de Tecnologia E Desenvolvimento Regional, Universidade Federal da Paraíba, Paraíba, João Pessoa, Brazil
| | - Estefânia Fernandes Garcia
- Departamento de Gastronomia, Centro de Tecnologia E Desenvolvimento Regional, Universidade Federal da Paraíba, Paraíba, João Pessoa, Brazil
| | - Evandro Leite de Souza
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I, João Pessoa, Paraíba, Brazil.
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15
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Characterization of Lactic Acid Bacteria in Raw Buffalo Milk: a Screening for Novel Probiotic Candidates and Their Transcriptional Response to Acid Stress. Probiotics Antimicrob Proteins 2020; 13:468-483. [PMID: 32829420 DOI: 10.1007/s12602-020-09700-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Lactic acid bacteria (LAB) are important microorganisms for the food industry due to their functional activity, as starters and potential probiotic strains. With that in mind, we explored the LAB diversity in raw buffalo milk, screening for novel potential probiotic strains. A total of 11 strains were identified by combination of MALDI-TOF and partial 16S rDNA sequencing and selected as potential probiotic candidates. Bacteria innocuity assessment was performed by determining antimicrobial susceptibility and the presence of virulence factors. Antagonism activity against Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes and Staphylococcus aureus was assessed, as well as milk proteolytic activity and exopolysaccharides production. Seven strains were identified as innocuous and two of them, Lactobacillus rhamnosus LB1.5 and Lactobacillus paracasei LB6.4 were selected for further probiotic potential analyses. Both strains demonstrated adhesion ability to Caco-2 cells, coaggregated with S. aureus and E. coli and maintained cell viability after gastrointestinal simulation in vitro, suggesting their probiotic potential. Furthermore, the transcriptional response of Lact. rhamnosus LB1.5 and Lact. paracasei LB6.4 to in vitro acid stress was assessed by RT-qPCR targeting seven genes related to adhesion, aggregation, stress tolerance, DNA repair and central metabolism. The association between the transcriptional responses and the maintenance of cell viability after gastrointestinal simulation highlights the genetic ability as probiotic of the two selected strains. Finally, we have concluded that Lact. rhamnosus LB1.5 and Lact. paracasei LB6.4 are important probiotic candidates to further in vivo studies.
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16
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O'Grady J, Cronin U, Tierney J, Piterina AV, O'Meara E, Wilkinson MG. Gaps in the assortment of rapid assays for microorganisms of interest to the dairy industry. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:1-56. [PMID: 32948264 PMCID: PMC7426214 DOI: 10.1016/bs.aambs.2020.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This review presents the results of a study into the offering of rapid microbial detection assays to the Irish dairy industry. At the outset, a consultation process was undertaken whereby key stakeholders were asked to compile a list of the key microorganisms of interest to the sector. The resultant list comprises 19 organisms/groups of organisms divided into five categories: single pathogenic species (Cronobacter sakazakii, Escherichia coli and Listeria monocytogenes); genera containing pathogenic species (Bacillus, Clostridium, Listeria, Salmonella; Staphylococcus); broad taxonomic groupings (Coliforms, Enterobacteriaceae, fecal Streptococci, sulfite reducing bacteria/sulfite reducing Clostridia [SRBs/SRCs], yeasts and molds); organisms displaying certain growth preferences or resistance as regards temperature (endospores, psychrotrophs, thermodurics, thermophiles); indicators of quality (total plate count, Pseudomonas spp.). A survey of the rapid assays commercially available for the 19 organisms/groups of organisms was conducted. A wide disparity between the number of rapid tests available was found. Four categories were used to summarize the availability of rapid assays per organism/group of organisms: high coverage (>15 assays available); medium coverage (5-15 assays available); low coverage (<5 assays available); no coverage (0 assays available). Generally, species or genera containing pathogens, whose presence is regulated-for, tend to have a good selection of commercially available rapid assays for their detection, whereas groups composed of heterogenous or even undefined genera of mainly spoilage organisms tend to be "low coverage" or "no coverage." Organisms/groups of organisms with "low coverage" by rapid assays include: Clostridium spp.; fecal Streptococci; and Pseudomonas spp. Those with "no coverage" by rapid assays include: endospores; psychrotrophs; SRB/SRCs; thermodurics; and thermophiles. An important question is: why have manufacturers of rapid microbiological assays failed to respond to the necessity for rapid methods for these organisms/groups of organisms? The review offers explanations, ranging from the technical difficulty involved in detecting as broad a group as the thermodurics, which covers the spores of multiple sporeforming genera as well at least six genera of mesophilic nonsporeformers, to the taxonomically controversial issue as to what constitutes a fecal Streptococcus or SRBs/SRCs. We review two problematic areas for assay developers: validation/certification and the nature of dairy food matrices. Development and implementation of rapid alternative test methods for the dairy industry is influenced by regulations relating to both the microbiological quality standards and the criteria alternative methods must meet to qualify as acceptable test methods. However, the gap between the certification of developer's test systems as valid alternative methods in only a handful of representative matrices, and the requirement of dairy industries to verify the performance of alternative test systems in an extensive and diverse range of dairy matrices needs to be bridged before alternative methods can be widely accepted and adopted in the dairy industry. This study concludes that many important dairy matrices have effectively been ignored by assay developers.
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Affiliation(s)
- John O'Grady
- Dairy Processing Technology Centre, University of Limerick, Limerick, Ireland
| | - Ultan Cronin
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.
| | - Joseph Tierney
- Glanbia Ingredients Ireland, Ballyragget, Co. Kilkenny, Ireland
| | - Anna V Piterina
- Dairy Processing Technology Centre, University of Limerick, Limerick, Ireland
| | - Elaine O'Meara
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Martin G Wilkinson
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
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17
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Yefet E, Colodner R, Strauss M, Gam Ze Letova Y, Nachum Z. A Randomized Controlled Open Label Crossover Trial to Study Vaginal Colonization of Orally Administered Lactobacillus Reuteri RC-14 and Rhamnosus GR-1 in Pregnant Women at High Risk for Preterm Labor. Nutrients 2020; 12:nu12041141. [PMID: 32325794 PMCID: PMC7230520 DOI: 10.3390/nu12041141] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/21/2022] Open
Abstract
Lactobacilli administration has been suggested for the treatment and prevention of bacterial vaginosis, which increases the risk for preterm birth. We aimed to evaluate the vaginal colonization of lactobacilli orally administered to pregnant women at risk for preterm birth. We performed a randomized and controlled crossover study between January 2016 and May 2017. Forty pregnant women at high risk for preterm birth with normal vaginal flora (Nugent score ≤ 3) were randomized to either receive two oral capsules/day each containing 5 × 109Lactobacilli (L.) rhamnosus GR-1 and L. reuteri RC-14 (n = 20) or no treatment (n = 20) for 2 months. Treatments were then crossed over for an additional two months. A vaginal examination and swabbing were performed for assessment of bacterial vaginosis at baseline and every month until study completion. At the same time points, vaginal samples were cultured and subjected to matrix-assisted-laser-desorption/ionization-time-of-flight-mass-spectrometry (MALDI TOF-MS) for the detection of the specific bacterial strains contained in the capsules. The primary endpoint was the presence of the administered lactobacilli strains in the vagina during the first two months of follow-up. Thirty-eight women completed the study. During the first two months of treatment, L. rhamnosus GR-1 was detected in one (5%) woman on the probiotic treatment and 2 (11%) women receiving no treatment (p = 0.6). L. rhamnosus GR-1 was detected in vaginal samples of 4 (11%) women during probiotic treatment (of both groups) and L. reuteri RC-14 was not detected in any samples. The rest of the endpoints were not different between the groups. Altogether, vaginal colonization of lactobacilli following oral administration is low during pregnancy.
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Affiliation(s)
- Enav Yefet
- Department of Obstetrics & Gynecology, Emek Medical Center, Afula 1834111, Israel; (Y.G.Z.L.); (Z.N.)
- Department of Obstetrics & Gynecology, Baruch Padeh Medical Center Poriya, Tiberias 1410000, Israel
- Faculty of Medicine in Galilee, Bar-Ilan University, Safed 1310000, Israel
- Correspondence: ; Tel.: +972-4-649-4516; Fax: +972-649-4-5483
| | - Raul Colodner
- Microbiology Laboratory, Emek Medical Center, Afula 1834111, Israel; (R.C.); (M.S.)
| | - Merav Strauss
- Microbiology Laboratory, Emek Medical Center, Afula 1834111, Israel; (R.C.); (M.S.)
| | - Yifat Gam Ze Letova
- Department of Obstetrics & Gynecology, Emek Medical Center, Afula 1834111, Israel; (Y.G.Z.L.); (Z.N.)
| | - Zohar Nachum
- Department of Obstetrics & Gynecology, Emek Medical Center, Afula 1834111, Israel; (Y.G.Z.L.); (Z.N.)
- Rappaport Faculty of Medicine, Technion, Haifa 3200003, Israel
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18
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Gantzias C, Lappa IK, Aerts M, Georgalaki M, Manolopoulou E, Papadimitriou K, De Brandt E, Tsakalidou E, Vandamme P. MALDI-TOF MS profiling of non-starter lactic acid bacteria from artisanal cheeses of the Greek island of Naxos. Int J Food Microbiol 2020; 323:108586. [PMID: 32199192 DOI: 10.1016/j.ijfoodmicro.2020.108586] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 01/27/2020] [Accepted: 03/07/2020] [Indexed: 12/25/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS), a culture based alternative for microbial diversity studies, is an attractive tool to dereplicate large numbers of isolates to a smaller set of representatives for downstream characterization. In the present study, MALDI-TOF MS, combined with a database of reference spectra compiled in previous studies, was applied to identify 88 non-starter lactic acid bacteria (NSLAB) isolated from 18 samples of four different artisanal cheeses produced in the Island of Naxos, Greece, from raw sheep and goat milk without the addition of starters. Eighty-four isolates (95.5%) could be identified directly via MALDI-TOF MS. Lactobacillus brevis and Lactobacillus plantarum were the dominant species, followed by Lactococcus lactis, Leuconostoc mesenteroides Lactobacillus paracasei, Lactobacillus rhamnosus, Pediococcus pentosaceus and Enterococcus faecium. The remaining four isolates represented species present in the database; however, within-species diversity was insufficiently covered. Additionally, pheS sequencing was applied to confirm identification.
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Affiliation(s)
- Charalampos Gantzias
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Gent, Belgium; Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Iliada K Lappa
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Gent, Belgium; Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Maarten Aerts
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Marina Georgalaki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Eugenia Manolopoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Kostas Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Evie De Brandt
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece.
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Gent, Belgium
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19
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Vermeulen MJ, Luijendijk A, Toledo L, Kaam AH, Reiss IKM. Quality of probiotic products for preterm infants: Contamination and missing strains. Acta Paediatr 2020; 109:276-279. [PMID: 31423636 DOI: 10.1111/apa.14976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/18/2019] [Accepted: 08/16/2019] [Indexed: 12/11/2022]
Abstract
Probiotics are effective in reducing necrotising enterocolitis in preterm infants, but routine use is not generally adopted. We describe a safety issue concerning contamination by pathogenic bacteria and missing of labelled strains in a probiotic product widely used in neonatal care. We recommend all centres using probiotics in the care of vulnerable patients to consider product safety checks in addition to the quality reports of manufacturers. Meanwhile, clinicians and manufacturers should collaborate to define quality standards for probiotic products in clinical settings as long as specific international regulations are lacking.
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Affiliation(s)
- Marijn J. Vermeulen
- Division of Neonatology, Department of Paediatrics Erasmus MC Sophia Children's Hospital Rotterdam The Netherlands
| | - Ad Luijendijk
- Department of Medical Microbiology and Infectious Diseases Erasmus MC Rotterdam The Netherlands
| | - Letty Toledo
- Department of Neonatology, Emma Children's Hospital Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
| | - Anton H. Kaam
- Department of Neonatology, Emma Children's Hospital Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
| | - Irwin K. M. Reiss
- Division of Neonatology, Department of Paediatrics Erasmus MC Sophia Children's Hospital Rotterdam The Netherlands
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20
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Treven P, Mahnič A, Rupnik M, Golob M, Pirš T, Matijašić BB, Lorbeg PM. Evaluation of Human Milk Microbiota by 16S rRNA Gene Next-Generation Sequencing (NGS) and Cultivation/MALDI-TOF Mass Spectrometry Identification. Front Microbiol 2019; 10:2612. [PMID: 31803156 PMCID: PMC6872673 DOI: 10.3389/fmicb.2019.02612] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
The aim of the present study was to characterize human milk microbiota (HMM) with 16S rRNA gene amplicon next-generation sequencing and cultivation/matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) identification approaches. We analyzed 31 human milk samples from healthy Slovenian mothers. To check the accuracy of MALDI-TOF MS identification, several colonies representing most abundant genera and those, which could not be reliably identified by MALDI-TOF, were subjected to Sanger sequencing of their 16S rRNA gene. We showed that cultivation/MALDI-TOF MS was a suitable tool for culture-dependent determination of HMM. With both approaches, Staphylococcus and Streptococcus were found as predominant genera in HMM and the abundance of Staphylococcus was associated with decreased microbial diversity. In addition, we characterized factors that might influence HMM. The use of a breast pump was significantly associated with composition of HMM, lower microbial load, and higher abundance of cultivable staphylococci. Moreover, our study suggests that administration of probiotics to the suckling infant might influence HMM by increased abundance of lactobacilli and the presence of viable probiotic bacteria in human milk. However, since our study was observational with relatively small sample size, more targeted studies are needed to study possible transfer of probiotics to the mammary gland via an external route and the physiological relevance of these events.
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Affiliation(s)
- Primož Treven
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
| | - Aleksander Mahnič
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Majda Golob
- Faculty of Veterinary Medicine, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Tina Pirš
- Faculty of Veterinary Medicine, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Bojana Bogovič Matijašić
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Mohar Lorbeg
- Department of Animal Science, Biotechnical Faculty, Institute of Dairy Science and Probiotics, University of Ljubljana, Ljubljana, Slovenia
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21
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Seol D, Jhang SY, Kim H, Kim SY, Kwak HS, Kim SH, Lee W, Park S, Kim H, Cho S, Kwak W. Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data. Front Microbiol 2019; 10:1683. [PMID: 31440213 PMCID: PMC6693478 DOI: 10.3389/fmicb.2019.01683] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 07/08/2019] [Indexed: 11/13/2022] Open
Abstract
Identifying the microbes present in probiotic products is an important issue in product quality control and public health. The most common methods used to identify genera containing species that produce lactic acid are matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA sequence analysis. However, the high cost of operation, difficulty in distinguishing between similar species, and limitations of the current sequencing technologies have made it difficult to obtain accurate results using these tools. To overcome these problems, a whole-genome shotgun sequencing approach has been developed along with various metagenomic classification tools. Widely used tools include the marker gene and k-mer methods, but their inevitable false-positives (FPs) hampered an accurate analysis. We therefore, designed a coverage-based pipeline to reduce the FP problem and to achieve a more reliable identification of species. The coverage-based pipeline described here not only shows higher accuracy for the detection of species and proportion analysis, based on mapping depth, but can be applied regardless of the sequencing platform. We believe that the coverage-based pipeline described in this study can provide appropriate support for probiotic quality control, addressing current labeling issues.
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Affiliation(s)
- Donghyeok Seol
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - So Yun Jhang
- C&K Genomics, Songpa-gu, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Hyaekang Kim
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Se-Young Kim
- R&D Center, CTCBIO, Inc., Hwaseong-si, South Korea
| | - Hyo-Sun Kwak
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Soon Han Kim
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Woojung Lee
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Sewook Park
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Heebal Kim
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Seoae Cho
- C&K Genomics, Songpa-gu, South Korea
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22
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Reliable identification of lactic acid bacteria by targeted and untargeted high-resolution tandem mass spectrometry. Food Chem 2019; 285:111-118. [DOI: 10.1016/j.foodchem.2019.01.127] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/26/2018] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
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23
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Ayala DI, Cook PW, Franco JG, Bugarel M, Kottapalli KR, Loneragan GH, Brashears MM, Nightingale KK. A Systematic Approach to Identify and Characterize the Effectiveness and Safety of Novel Probiotic Strains to Control Foodborne Pathogens. Front Microbiol 2019; 10:1108. [PMID: 31156609 PMCID: PMC6533568 DOI: 10.3389/fmicb.2019.01108] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/01/2019] [Indexed: 12/16/2022] Open
Abstract
A total of 44 lactic acid bacteria (LAB) strains originally isolated from cattle feces and different food sources were screened for their potential probiotic features. The antimicrobial activity of all isolates was tested by well-diffusion assay and competitive exclusion on broth against Salmonella Montevideo, Escherichia coli O157:H7 and Listeria monocytogenes strain N1-002. Thirty-eight LAB strains showed antagonistic effect against at least one of the pathogens tested in this study. Improved inhibitory effect was observed against L. monocytogenes with zones of inhibition up to 24 mm when LAB overnight cultures were used, and up to 21 mm when cell-free filtrates were used. For E. coli O157:H7 and Salmonella maximum inhibitions of 12 and 11.5 mm were observed, respectively. On broth, 43 strains reduced L. monocytogenes up to 9.06 log10 CFU/ml, 41 reduced E. coli O157:H7 up to 0.84 log10 CFU/ml, and 32 reduced Salmonella up to 0.94 log10 CFU/ml 24 h after co-inoculation. Twenty-eight LAB isolates that exhibited the highest inhibitory effect among pathogens were further analyzed to determine their antimicrobial resistance profile, adhesion potential, and cytotoxicity to Caco-2 cells. All LAB strains tested were susceptible to ampicillin, linezolid, and penicillin. Twenty-six were able to adhere to Caco-2 cells, five were classified as highly adhesive with > 40 bacterial cells/Caco-2 cells. Low cytotoxicity percentages were observed for the candidate LAB strains with values ranging from -5 to 8%. Genotypic identification by whole genome sequencing confirmed all as members of the LAB group; Enterococcus was the genus most frequently isolated with 21 isolates, followed by Pediococcus with 4, and Lactobacillus with 3. In this study, a systematic approach was used for the improved identification of novel LAB strains able to exert antagonistic effect against important foodborne pathogens. Our findings suggest that the selected panel of LAB probiotic strains can be used as biocontrol cultures to inhibit and/or reduce the growth of L. monocytogenes, Salmonella, and E. coli O157:H7 in different matrices, and environments.
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Affiliation(s)
- Diana I Ayala
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States
| | - Peter W Cook
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States.,Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jorge G Franco
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States
| | - Marie Bugarel
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States
| | - Kameswara R Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Guy H Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States
| | - Mindy M Brashears
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States
| | - Kendra K Nightingale
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, United States
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24
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Angelakis E, Bachar D, Yasir M, Musso D, Djossou F, Melenotte C, Robert C, Davoust B, Gaborit B, Azhar E, Bibi F, Dutour A, Raoult D. Comparison of the gut microbiota of obese individuals from different geographic origins. New Microbes New Infect 2019; 27:40-47. [PMID: 30581574 PMCID: PMC6296163 DOI: 10.1016/j.nmni.2018.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023] Open
Abstract
Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.
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Affiliation(s)
- E. Angelakis
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - D. Bachar
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - M. Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - D. Musso
- Unit of Emerging Infectious Diseases, Institut Louis Malardé, Tahiti, French Polynesia
| | - F. Djossou
- Centre Hospitalier de Cayenne Andree Rosemon, Cayenne, French Guiana
| | - C. Melenotte
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - C. Robert
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - B. Davoust
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - B. Gaborit
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
- Inserm U1062, INRA U1260, Faculté de Médecine, Marseille, France
| | - E.I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - F. Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Dutour
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
- Inserm U1062, INRA U1260, Faculté de Médecine, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
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25
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Angelakis E, Bachar D, Yasir M, Musso D, Djossou F, Gaborit B, Brah S, Diallo A, Ndombe G, Mediannikov O, Robert C, Azhar E, Bibi F, Nsana N, Parra HJ, Akiana J, Sokhna C, Davoust B, Dutour A, Raoult D. Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals. New Microbes New Infect 2019; 27:14-21. [PMID: 30555706 PMCID: PMC6276622 DOI: 10.1016/j.nmni.2018.10.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/18/2018] [Accepted: 10/25/2018] [Indexed: 01/16/2023] Open
Abstract
There is a significant gap in our knowledge of the microbe-host relationship between urban and traditional rural populations. We conducted a large-scale study to examine the gut microbiota of different traditional rural and urban lifestyles in human populations. Using high-throughput 16S ribosomal RNA gene amplicon sequencing, we tested urban French, Saudi, Senegalese, Nigerian and Polynesian individuals as well as individuals living in traditional rural societies, including Amazonians from French Guiana, Congolese Pygmies, Saudi Bedouins and Algerian Tuaregs. The gut microbiota from individuals living in traditional rural settings clustered differently and presented significantly higher diversity than those of urban populations (p 0.01). The bacterial taxa identified by class analysis as contributing most significantly to each cluster were Phascolarctobacterium for traditional rural individuals and Bifidobacterium for urban individuals. Spirochaetae were only present in the gut microbiota of individuals from traditional rural societies, and the gut microbiota of all traditional rural populations was enriched with Treponema succinifaciens. Cross-transmission of Treponema from termites or swine to humans or the increased use of antibiotics in nontraditional populations may explain why Treponema is present only in the gut microbiota of traditional rural populations.
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Affiliation(s)
- E. Angelakis
- Aix-Marseille Université, IRD, APHM, VITROME, IHU Méditerranée Infection, France
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - D. Bachar
- Aix-Marseille Université, IRD, APHM, VITROME, IHU Méditerranée Infection, France
| | - M. Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - D. Musso
- Unit of Emerging Infectious Diseases, Institut Louis Malardé, Tahiti, French Polynesia
| | - F. Djossou
- Centre Hospitalier de Cayenne Andree Rosemon, Cayenne, French Guiana
| | - B. Gaborit
- NORT, Aix-Marseille Université, INSERM, INRA, France
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
- Hôpital National de Niamey, Niamey, Niger
| | - S. Brah
- Service de Médecine Interne et Générale, Niger
| | - A. Diallo
- Aix-Marseille Université, IRD, APHM, VITROME, IHU Méditerranée Infection, France
| | - G.M. Ndombe
- Laboratoire national de santé publique, Brazzaville, République populaire du Congo
| | - O. Mediannikov
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, France
| | - C. Robert
- Aix-Marseille Université, IRD, APHM, VITROME, IHU Méditerranée Infection, France
| | - E.I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - F. Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - N.S. Nsana
- Laboratoire national de santé publique, Brazzaville, République populaire du Congo
| | - H.-J. Parra
- Laboratoire national de santé publique, Brazzaville, République populaire du Congo
| | - J. Akiana
- Laboratoire national de santé publique, Brazzaville, République populaire du Congo
| | - C. Sokhna
- Aix-Marseille Université, IRD, APHM, VITROME, IHU Méditerranée Infection, France
| | - B. Davoust
- Aix-Marseille Université, IRD, APHM, VITROME, IHU Méditerranée Infection, France
| | - A. Dutour
- NORT, Aix-Marseille Université, INSERM, INRA, France
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, France
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26
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Abat C, Rolain JM, Colson P. Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa. New Microbes New Infect 2018; 26:S37-S42. [PMID: 30402242 PMCID: PMC6205566 DOI: 10.1016/j.nmni.2018.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 07/02/2018] [Accepted: 08/22/2018] [Indexed: 12/25/2022] Open
Abstract
Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted.
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27
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Lin S, Bi X, Zhu S, Yin H, Li Z, Chen C. Dual-type hyperspectral microscopic imaging for the identification and analysis of intestinal fungi. BIOMEDICAL OPTICS EXPRESS 2018; 9:4496-4508. [PMID: 30615713 PMCID: PMC6157763 DOI: 10.1364/boe.9.004496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 05/21/2023]
Abstract
A method based on a dual-type (transmission and fluorescence) hyperspectral microscopic image system was developed to identify species of intestinal fungi. Living fungi are difficult to identify via transmission spectra or fluorescence spectra alone. We propose an identification method based on both fluorescence and transmission spectra that employs a series of image processing methods. Three species of intestinal fungi were used to evaluate the method. The results demonstrate that the specificity of the model trained with dual-type spectra was 98.36%, whereas the specificities achieved by training with fluorescence spectra and transmission spectra alone were 94.04% and 92.88%, respectively.
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Affiliation(s)
- Sifan Lin
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Guangzhou 510632, China
| | - Xiaolin Bi
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Guangzhou 510632, China
| | - Siqi Zhu
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Guangzhou 510632, China
- Guangdong Provincial Engineering Research Center of Crystal and Laser Technology, Guangzhou 510632, China
| | - Hao Yin
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Guangzhou 510632, China
| | - Zhen Li
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Guangzhou 510632, China
| | - Chenqiang Chen
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Guangzhou 510632, China
- Guangdong Provincial Engineering Research Center of Crystal and Laser Technology, Guangzhou 510632, China
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, China
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28
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Huang CH, Li SW, Huang L, Watanabe K. Identification and Classification for the Lactobacillus casei Group. Front Microbiol 2018; 9:1974. [PMID: 30186277 PMCID: PMC6113361 DOI: 10.3389/fmicb.2018.01974] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.,Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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29
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El-Jeni R, Böhme K, El Bour M, Calo-Mata P, Kefi R, Barros-Velázquez J, Bouhaouala-Zahar B. Rapid genus identification of selected lactic acid bacteria isolated from Mugil cephalis and Oreochromis niloticus organs using MALDI-TOF. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1357-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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30
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Devaux CA, Raoult D. The Microbiological Memory, an Epigenetic Regulator Governing the Balance Between Good Health and Metabolic Disorders. Front Microbiol 2018; 9:1379. [PMID: 29997595 PMCID: PMC6028609 DOI: 10.3389/fmicb.2018.01379] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/06/2018] [Indexed: 12/12/2022] Open
Abstract
If the transmission of biological information from one generation to the next is based on DNA, most heritable phenotypic traits such as chronic metabolic diseases, are not linked to genetic variation in DNA sequences. Non-genetic heritability might have several causes including epigenetic, parental effect, adaptive social learning, and influence of the ecological environment. Distinguishing among these causes is crucial to resolve major phenotypic enigmas. Strong evidence indicates that changes in DNA expression through various epigenetic mechanisms can be linked to parent-offspring resemblance in terms of sensitivity to metabolic diseases. Among non-genetic heritable traits, early nutrition could account for a long term deviant programming of genes expression responsible for metabolic diseases in adulthood. Nutrition could shape an inadequate gut microbiota (dysbiosis), triggering epigenetic deregulation of transcription which can be observed in chronic metabolic diseases. We review herein the evidence that dysbiosis might be a major cause of heritable epigenetic patterns found to be associated with metabolic diseases. By taking into account the recent advances on the gut microbiome, we have aggregated together different observations supporting the hypothesis that the gut microbiota could promote the molecular crosstalk between bacteria and surrounding host cells which controls the pathological epigenetic signature. We introduce for the first time the concept of "microbiological memory" as the main regulator of the epigenetic signatures, thereby indicating that different causes of non-genetic heritability can interact in complex pathways to produce inheritance.
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Affiliation(s)
- Christian A. Devaux
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
- Centre National de la Recherche Scientifique, Marseille, France
| | - Didier Raoult
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille University, Marseille, France
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31
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Ledina T, Golob M, Djordjević J, Magas V, Colovic S, Bulajic S. MALDI-TOF mass spectrometry for the identification of Serbian artisanal cheeses microbiota. J Verbrauch Lebensm 2018. [DOI: 10.1007/s00003-018-1164-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Temporal and Spatial Distribution of the Acetic Acid Bacterium Communities throughout the Wooden Casks Used for the Fermentation and Maturation of Lambic Beer Underlines Their Functional Role. Appl Environ Microbiol 2018; 84:AEM.02846-17. [PMID: 29352086 DOI: 10.1128/aem.02846-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/16/2018] [Indexed: 12/24/2022] Open
Abstract
Few data have been published on the occurrence and functional role of acetic acid bacteria (AAB) in lambic beer production processes, mainly due to their difficult recovery and possibly unknown role. Therefore, a novel aseptic sampling method, spanning both the spatial and temporal distributions of the AAB and their substrates and metabolites, was combined with a highly selective medium and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a high-throughput dereplication method followed by comparative gene sequencing for their isolation and identification, respectively. The AAB (Acetobacter species more than Gluconobacter species) proliferated during two phases of the lambic beer production process, represented by Acetobacter orientalis during a few days in the beginning of the fermentation and Acetobacter pasteurianus from 7 weeks until 24 months of maturation. Competitive exclusion tests combined with comparative genomic analysis of all genomes of strains of both species available disclosed possible reasons for this successive dominance. The spatial analysis revealed that significantly higher concentrations of acetic acid (from ethanol) and acetoin (from lactic acid) were produced at the tops of the casks, due to higher AAB counts and a higher metabolic activity of the AAB species at the air/liquid interface during the first 6 months of lambic beer production. In contrast, no differences in AAB species diversity occurred throughout the casks.IMPORTANCE Lambic beer is an acidic beer that is the result of a spontaneous fermentation and maturation process. Acidic beers are currently attracting attention worldwide. Part of the acidity of these beers is caused by acetic acid bacteria (AAB). However, due to their difficult recovery, they were never investigated extensively regarding their occurrence, species diversity, and functional role in lambic beer production. In the present study, a framework was developed for their isolation and identification using a novel aseptic sampling method in combination with matrix-assisted laser desorption ionization-time of flight mass spectrometry as a high-throughput dereplication technique followed by accurate molecular identification. The sampling method applied enabled us to take spatial differences into account regarding both enumerations and metabolite production. In this way, it was shown that more AAB were present and more acetic acid was produced at the air/liquid interface during a major part of the lambic beer production process. Also, two different AAB species were encountered, namely, Acetobacter orientalis at the beginning and Acetobacter pasteurianus in a later stage of the production process. This developed framework could also be applied for other fermentation processes.
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Vecchione A, Celandroni F, Mazzantini D, Senesi S, Lupetti A, Ghelardi E. Compositional Quality and Potential Gastrointestinal Behavior of Probiotic Products Commercialized in Italy. Front Med (Lausanne) 2018; 5:59. [PMID: 29564327 PMCID: PMC5845905 DOI: 10.3389/fmed.2018.00059] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/19/2018] [Indexed: 01/21/2023] Open
Abstract
Recent guidelines indicate that oral probiotics, living microorganisms able to confer a health benefit on the host, should be safe for human consumption, when administered in a sufficient amount, and resist acid and bile to exert their beneficial effects (e.g., metabolic, immunomodulatory, anti-inflammatory, competitive). This study evaluated quantitative and qualitative aspects and the viability in simulated gastric and intestinal juices of commercial probiotic formulations available in Italy. Plate counting and MALDI-TOF mass spectrometry were used to enumerate and identify the contained organisms. In vitro studies with two artificial gastric juices and pancreatin-bile salt solution were performed to gain information on the gastric tolerance and bile resistance of the probiotic formulations. Most preparations satisfied the requirements for probiotics and no contaminants were found. Acid resistance and viability in bile were extremely variable depending on the composition of the formulations in terms of contained species and strains. In conclusion, this study indicates good microbiological quality but striking differences in the behavior in the presence of acids and bile for probiotic formulations marketed in Italy.
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Affiliation(s)
- Alessandra Vecchione
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sonia Senesi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy,Research Center Nutraceuticals and Food for Health-Nutrafood, University of Pisa, Pisa, Italy,*Correspondence: Emilia Ghelardi,
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Huang CH, Huang L. Rapid species- and subspecies-specific level classification and identification of Lactobacillus casei group members using MALDI Biotyper combined with ClinProTools. J Dairy Sci 2018; 101:979-991. [DOI: 10.3168/jds.2017-13642] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/30/2017] [Indexed: 12/16/2022]
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Hilgarth M, Behr J, Vogel R. Monitoring of spoilage-associated microbiota on modified atmosphere packaged beef and differentiation of psychrophilic and psychrotrophic strains. J Appl Microbiol 2018; 124:740-753. [DOI: 10.1111/jam.13669] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/17/2017] [Accepted: 12/05/2017] [Indexed: 11/28/2022]
Affiliation(s)
- M. Hilgarth
- Technische Universität München; Lehrstuhl für Technische Mikrobiologie; Freising Germany
| | - J. Behr
- Technische Universität München; Lehrstuhl für Technische Mikrobiologie; Freising Germany
| | - R.F. Vogel
- Technische Universität München; Lehrstuhl für Technische Mikrobiologie; Freising Germany
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Wilson HL, Ong CW. Bifidobacterium longum vertebrodiscitis in a patient with cirrhosis and prostate cancer. Anaerobe 2017; 47:47-50. [PMID: 28408274 DOI: 10.1016/j.anaerobe.2017.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/07/2017] [Accepted: 04/08/2017] [Indexed: 11/30/2022]
Abstract
Bifidobacterium species are anaerobic, Gram-positive bacilli that colonize the human intestinal tract and oral cavity. They are an infrequent cause of invasive human infection. We report a case of Bifidobacterium longum lumbar vertebrodiscitis in a 71 year old man who was subsequently diagnosed with liver cirrhosis and prostate cancer. The clinical outcome was good following antibiotic treatment with penicillin and clindamycin. The laboratory identification of Bifidobacterium species and risk factors for invasive infection are discussed.
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Affiliation(s)
- Heather L Wilson
- Canberra Hospital and Health Services, PO Box 11, Woden, ACT 2606, Australia.
| | - Chong Wei Ong
- Canberra Hospital and Health Services, PO Box 11, Woden, ACT 2606, Australia
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Foschi C, Laghi L, Parolin C, Giordani B, Compri M, Cevenini R, Marangoni A, Vitali B. Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR. PLoS One 2017; 12:e0172483. [PMID: 28207855 PMCID: PMC5312945 DOI: 10.1371/journal.pone.0172483] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 02/07/2023] Open
Abstract
Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the ‘health-promoting’ significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species.
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Affiliation(s)
- Claudio Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Luca Laghi
- Centre of Foodomics, Department of Agro-Food Science and Technology, University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Barbara Giordani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Monica Compri
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | | | | | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Angelakis E. Weight gain by gut microbiota manipulation in productive animals. Microb Pathog 2016; 106:162-170. [PMID: 27836763 DOI: 10.1016/j.micpath.2016.11.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 06/23/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022]
Abstract
Antibiotics, prebiotics and probiotics are widely used as growth promoters in agriculture. In the 1940s, use of Streptomyces aureofaciens probiotics resulted in weight gain in animals, which led to the discovery of chlortetracycline. Tetracyclines, macrolides, avoparcin and penicillins have been commonly used in livestock agriculture to promote growth through increased food intake, weight gain, and improved herd health. Prebiotic supplements including oligosaccharides, fructooligosaccharides, and galactosyl-lactose improve the growth performance of animals. Probiotics used in animal feed are mainly bacterial strains of Gram-positive bacteria and have been effectively used for weight gain in chickens, pigs, ruminants and in aquaculture. Antibiotics, prebiotics and probiotics all modify the gut microbiota and the effect of a probiotic species on the digestive flora is probably determined by bacteriocin production. Regulations governing the introduction of novel probiotics and prebiotics vary by geographical region and bias is very common in industry-funded studies. Probiotic and prebiotic foods have been consumed for centuries, either as natural components of food, or as fermented foods and it is possible to cause the same weight gain effects in humans as in animals. This review presents the use of growth promoters in food-producing animals to influence food intake and weight gain.
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Affiliation(s)
- Emmanouil Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
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Morovic W, Hibberd AA, Zabel B, Barrangou R, Stahl B. Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases. Front Microbiol 2016; 7:1747. [PMID: 27857709 PMCID: PMC5093124 DOI: 10.3389/fmicb.2016.01747] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation “well defined strains,” encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species using plate counting and targeted genotyping. Strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS) of the 16S rRNA sequence using paired-end 2 × 250 bp Illumina MiSeq technology. Using these methods, we tested the hypothesis that products do contain the quantitative and qualitative list of labeled microbial species. We found that 17 samples (33%) were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58%) of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species, and un-labeled species. The HTS revealed that many blended products consisted predominantly of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis. These results highlight the need for reliable methods to determine the correct taxonomy and quantify the relative amounts of mixed microbial populations in commercial probiotic products.
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Affiliation(s)
- Wesley Morovic
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
| | - Ashley A Hibberd
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
| | - Bryan Zabel
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University Raleigh, NC, USA
| | - Buffy Stahl
- Genomics and Microbiome Science, DuPont Nutrition & Health Madison, WI, USA
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40
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Garcia EF, Luciano WA, Xavier DE, da Costa WCA, de Sousa Oliveira K, Franco OL, de Morais Júnior MA, Lucena BTL, Picão RC, Magnani M, Saarela M, de Souza EL. Identification of Lactic Acid Bacteria in Fruit Pulp Processing Byproducts and Potential Probiotic Properties of Selected Lactobacillus Strains. Front Microbiol 2016; 7:1371. [PMID: 27625647 PMCID: PMC5003889 DOI: 10.3389/fmicb.2016.01371] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/18/2016] [Indexed: 12/17/2022] Open
Abstract
This study aimed to identify lactic acid bacteria (LAB) in byproducts of fruit (Malpighia glabra L., Mangifera indica L., Annona muricata L., and Fragaria vesca L.) pulp processing. Fifty strains of LAB were identified using matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequence (16S rRNA) analysis. Species belonging to Lactobacillus genus were the predominant LAB in all fruit pulp processing byproducts. The average congruency between the MALDI-TOF MS and 16S rRNA in LAB species identification reached 86%. Isolates of L. plantarum, L. brevis, L. pentosus, L. lactis and L. mesenteroides were identified with 100% congruency. MALDI-TOF MS and 16S rRNA analysis presented 86 and 100% efficiency of LAB species identification, respectively. Further, five selected Lactobacillus strains (L. brevis 59, L. pentosus 129, L. paracasei 108, L. plantarum 49, and L. fermentum 111) were evaluated for desirable probiotic-related properties and growth behavior on two different cultivation media. The exposure to pH 2.0 sharply decreased the counts of the different Lactobacillus strains after a 1 or 2 h incubation, while varied decreases were noted after 3 h of exposure to pH 3.0. Overall, the exposure to pH 5.0 and to bile salts (0.15, 0.30, and 1.00%) did not decrease the counts of the Lactobacillus strains. All tested Lactobacillus strains presented inhibitory activity against Staphylococcus aureus, Salmonella Typhimurium, Salmonella Enteritidis, Listeria monocytogenes and Escherichia coli, and presented variable susceptibility to different antibiotics. The selected Lactobacillus strains presented satisfactory and reproducible growth behavior. In conclusion, MALDI-TOF MS and 16S rRNA analysis revealed high efficiency and congruency for LAB species identification, and the selected Lactobacillus strains may be candidates for further investigation of novel probiotic strains.
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Affiliation(s)
- Estefânia F Garcia
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Winnie A Luciano
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Danilo E Xavier
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Whyara C A da Costa
- Laboratório de Processos Microbianos em Alimentos, Departamento de Engenharia de Alimentos, Universidade Federal da Paraíba João Pessoa, Brazil
| | | | - Octávio L Franco
- Laboratório de Genômica e Proteômica, Universidade Católica de Brasília Brasília, Brazil
| | - Marcos A de Morais Júnior
- Grupo Interdepartamental de Pesquisa em Engenharia Metabólica, Departamento de Genética, Universidade Federal de Pernambuco Recife, Brazil
| | - Brígida T L Lucena
- Grupo Interdepartamental de Pesquisa em Engenharia Metabólica, Departamento de Genética, Universidade Federal de Pernambuco Recife, Brazil
| | - Renata C Picão
- Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Marciane Magnani
- Laboratório de Processos Microbianos em Alimentos, Departamento de Engenharia de Alimentos, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Maria Saarela
- VTT Technical Research Centre of Finland Espoo, Finland
| | - Evandro L de Souza
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
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Dec M, Puchalski A, Urban-Chmiel R, Wernicki A. 16S-ARDRA and MALDI-TOF mass spectrometry as tools for identification of Lactobacillus bacteria isolated from poultry. BMC Microbiol 2016; 16:105. [PMID: 27296852 PMCID: PMC4906599 DOI: 10.1186/s12866-016-0732-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/06/2016] [Indexed: 12/13/2022] Open
Abstract
Background The objective of our study is to evaluate the potential use of Amplified 16S Ribosomal DNA Restriction Analysis (16S-ARDRA) and MALDI-TOF mass spectrometry (MS) as methods for species identification of Lactobacillus strains in poultry. Results A total of 80 Lactobacillus strains isolated from the cloaca of chicken, geese and turkeys were identified to the species level by MALDI-TOF MS (on-plate extraction method) and 16S-ARDRA. The two techniques produced comparable classification results, some of which were additionally confirmed by sequencing of 16S rDNA. MALDI-TOF MS enabled rapid species identification but produced more than one reliable identification result for 16.25 % of examined strains (mainly of the species L. johnsonii). For 30 % of isolates intermediate log(scores) of 1.70–1.99 were obtained, indicating correct genus identification but only presumptive species identification. The 16S-ARDRA protocol was based on digestion of 16S rDNA with the restriction enzymes MseI, HinfI, MboI and AluI. This technique was able to distinguish 17 of the 19 Lactobacillus reference species tested and enabled identification of all 80 wild isolates. L. salivarius dominated among the 15 recognized species, followed by L. johnsonii and L. ingluviei. Conclusions The MALDI-TOF MS and 16S-ARDRA assays are valuable tools for the identification of avian lactobacilli to the species level. MALDI-TOF MS is a fast, simple and cost-effective technique, and despite generating a high percentage of results with a log(score) <2.00, the on-plate extraction method is characterized by high-performance. For samples for which Biotyper produces more than one reliable result, MALDI-TOF MS must be used in combination with genotypic techniques to achieve unambiguous results. 16S-ARDRA is simple, repetitive method with high power of discrimination, whose sole limitation is its inability to discriminate between species with very high 16S rDNA sequence homology, such as L. casei and L. zeae. The assays can be used for discrimination of Lactobacillus bacteria from different habitats.
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Affiliation(s)
- Marta Dec
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033, Lublin, Poland.
| | - Andrzej Puchalski
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033, Lublin, Poland
| | - Renata Urban-Chmiel
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033, Lublin, Poland
| | - Andrzej Wernicki
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033, Lublin, Poland
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Tamang JP, Watanabe K, Holzapfel WH. Review: Diversity of Microorganisms in Global Fermented Foods and Beverages. Front Microbiol 2016; 7:377. [PMID: 27047484 PMCID: PMC4805592 DOI: 10.3389/fmicb.2016.00377] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/08/2016] [Indexed: 01/03/2023] Open
Abstract
Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups ("phylotypes") may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.
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Affiliation(s)
- Jyoti P. Tamang
- Department of Microbiology, School of Life Sciences, Sikkim UniversityTadong, India
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan UniversityTaipei, Taiwan
| | - Wilhelm H. Holzapfel
- Advance Green Energy and Environment Institute, Handong Global UniversityPohang-si, South Korea
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Validating bifidobacterial species and subspecies identity in commercial probiotic products. Pediatr Res 2016; 79:445-52. [PMID: 26571226 PMCID: PMC4916961 DOI: 10.1038/pr.2015.244] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The ingestion of probiotics to attempt to improve health is increasingly common; however, quality control of some commercial products can be limited. Clinical practice is shifting toward the routine use of probiotics to aid in prevention of necrotizing enterocolitis in premature infants, and probiotic administration to term infants is increasingly common to treat colic and/or prevent atopic disease. Since bifidobacteria dominate the feces of healthy breast-fed infants, they are often included in infant-targeted probiotics. METHODS We evaluated 16 probiotic products to determine how well their label claims describe the species of detectable bifidobacteria in the product. Recently developed DNA-based methods were used as a primary means of identification, and were confirmed using culture-based techniques. RESULTS We found that the contents of many bifidobacterial probiotic products differ from the ingredient list, sometimes at a subspecies level. Only 1 of the 16 probiotics perfectly matched its bifidobacterial label claims in all samples tested, and both pill-to-pill and lot-to-lot variation were observed. CONCLUSION Given the known differences between various bifidobacterial species and subspecies in metabolic capacity and colonization abilities, the prevalence of misidentified bifidobacteria in these products is cause for concern for those involved in clinical trials and consumers of probiotic products.
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Angelakis E, Lagier JC. Samples and techniques highlighting the links between obesity and microbiota. Microb Pathog 2016; 106:119-126. [PMID: 26828871 DOI: 10.1016/j.micpath.2016.01.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/23/2016] [Accepted: 01/28/2016] [Indexed: 12/17/2022]
Abstract
The composition of gut microbiota and its relationship to human health, particularly its links with obesity remain an ongoing challenge for scientists. The current gold standard for exploring human gut microbiota consists of using stool samples and only applying next generations sequencing techniques, which sometimes generate contradictory results. Here, we comprehensively describe nutrient absorption, fat digestion, carbohydrate and protein absorption, demonstrating that absorption of these diverse nutrients occurs mainly in the stomach and small intestine. Indeed, bariatric surgery, including Roux-en-Y, removes part of the upper intestine, resulting in weight loss, while colonic surgery is associated with a stable weight. However, most studies only use stool samples rather than small intestine samples because of the easy with which this can be accessed. Metagenomics studies are associated with several biases such as extraction and primer biases and depth bias, including the more modern platforms. High-throughput culture-dependent techniques, such as culturomics, which uses rapid identification methods such as MALDI-TOF, remain time-consuming, but have demonstrated their complementarity with molecular techniques. In conclusion, we believe that a comprehensive analysis of the relationships between obesity and gut microbiota requires large-scale studies coupling metagenomics and culture-dependent research, in order to analyse both small intestine and stool samples.
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Affiliation(s)
- Emmanouil Angelakis
- Aix-Marseille Université URMITE, UM63, IHU Méditerranée Infection, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université URMITE, UM63, IHU Méditerranée Infection, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France.
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Khonsari S, Suganthy M, Burczynska B, Dang V, Choudhury M, Pachenari A. A comparative study of bifidobacteria in human babies and adults. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2015; 35:97-103. [PMID: 27200263 PMCID: PMC4858883 DOI: 10.12938/bmfh.2015-006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
Abstract
The composition and diversity of the gut microbiota are known to be different between babies and adults. The
aim of this project was to compare the level of bifidobacteria between babies and adults and to investigate
the influence of lifestyle factors on the level of this bacterium in the gut. During this study, the levels of
bifidobacteria in 10 human babies below 2 years of age were compared with that of 10 human adults above 40
years. The level of bifidobacteria proved to be significantly higher in babies in comparison with adults. This
investigation concluded that a combination of several factors, such as age, diet, and BMI, has an important
effect on the level of bifidobacteria in adults, while in babies, a combination of diet and age may influence
the level of intestinal bifidobacteria.
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Affiliation(s)
- Shadi Khonsari
- School of Science and Technology, Middlesex University, Town Hall The Burroughs, Hendon, London NW4 4BT, UK
| | - Mayuran Suganthy
- School of Science and Technology, Middlesex University, Town Hall The Burroughs, Hendon, London NW4 4BT, UK
| | - Beata Burczynska
- School of Science and Technology, Middlesex University, Town Hall The Burroughs, Hendon, London NW4 4BT, UK
| | - Vu Dang
- School of Science and Technology, Middlesex University, Town Hall The Burroughs, Hendon, London NW4 4BT, UK
| | - Manika Choudhury
- School of Science and Technology, Middlesex University, Town Hall The Burroughs, Hendon, London NW4 4BT, UK
| | - Azra Pachenari
- School of Science and Technology, Middlesex University, Town Hall The Burroughs, Hendon, London NW4 4BT, UK
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46
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 770] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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Yasir M, Angelakis E, Bibi F, Azhar EI, Bachar D, Lagier JC, Gaborit B, Hassan AM, Jiman-Fatani AA, Alshali KZ, Robert C, Dutour A, Raoult D. Comparison of the gut microbiota of people in France and Saudi Arabia. Nutr Diabetes 2015; 5:e153. [PMID: 25915742 PMCID: PMC4423199 DOI: 10.1038/nutd.2015.3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/27/2015] [Accepted: 03/15/2015] [Indexed: 12/18/2022] Open
Abstract
Background/Objectives: The gut microbiota contributes to energy acquisition from food, and changes in the gut microbiome are associated with obesity. The eating habits of Saudis are much different than those of Europeans, and our objective was to compare the fecal microbiota of obese and normal weight Saudis and French. Subjects/Methods: Illumina MiSeq deep sequencing was used to test the gut microbiota of 9 normal weight and 9 obese individuals from Saudi Arabia and 16 normal weight and 12 obese individuals from France. Results: Obese French possessed significantly more relative Proteobacteria (P=0.002) and Bacteroidetes (P=0.05) and had lower richness and biodiversity at all the operational taxonomic unit (OTU) cutoffs (P<0.05) than normal weight French. Obese Saudis possessed significantly more Firmicutes (P=0.001) without a difference in richness (P=0.2) and biodiversity (P=0.3) compared with normal weight Saudis. We found a common bacterial species core of 23 species existing in ⩾50% of obese and normal weight Saudis and 29 species in ⩾50% of obese and normal weight French. Actinomyces odontolyticus, Escherichia coli and Ruminococcus obeum were present in at least 50% of all individuals tested. French individuals had significantly higher richness and biodiversity compared with Saudis at all the OTU cutoffs (P<0.05). Conclusion: Microbiota differences between obese and normal weight French were not similar to those between obese and normal weight Saudis. The studies of different populations can result in contrasting data regarding the associations of the gut microbiota and obesity.
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Affiliation(s)
- M Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - F Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E I Azhar
- 1] Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia [2] Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - D Bachar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - B Gaborit
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
| | - A M Hassan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - A A Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - K Z Alshali
- Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - A Dutour
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Anderson AC, Sanunu M, Schneider C, Clad A, Karygianni L, Hellwig E, Al-Ahmad A. Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing. BMC Microbiol 2014; 14:312. [PMID: 25495549 PMCID: PMC4272787 DOI: 10.1186/s12866-014-0312-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/25/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. RESULTS Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. CONCLUSION MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
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Affiliation(s)
- Annette Carola Anderson
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Mohamed Sanunu
- Department of Hygiene and Microbiology, Albert-Ludwigs-University, Hermann-Herder-Str. 11, Freiburg, Germany.
| | - Christian Schneider
- Department of Hygiene and Microbiology, Albert-Ludwigs-University, Hermann-Herder-Str. 11, Freiburg, Germany.
| | - Andreas Clad
- Department for Gynaecology, Medical Center, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Lamprini Karygianni
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Elmar Hellwig
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
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Angelakis E, Yasir M, Azhar EI, Papadioti A, Bibi F, Aburizaiza AS, Metidji S, Memish ZA, Ashshi AM, Hassan AM, Harakeh S, Gautret P, Raoult D. MALDI-TOF mass spectrometry and identification of new bacteria species in air samples from Makkah, Saudi Arabia. BMC Res Notes 2014; 7:892. [PMID: 25491533 PMCID: PMC4295573 DOI: 10.1186/1756-0500-7-892] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 11/25/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND During the Hajj season, respiratory symptoms are very common among pilgrims. Here, we investigated the viable bacterial population in air samples collected around the slaughterhouses used during the Hajj. METHODS AND RESULTS We collected air samples on three days from four different sites: slaughterhouses at Al-Kakia, Al-Meaisim and Al-Sharaia, and from a waste disposal area designated for the remnants of slaughter. Samples were cultured on blood agar plates for 48 h, and bacterial isolates were identified using MALDI-TOF MS. A dendrogram using the spectra of the unidentified bacterial species was constructed, and PCR amplification and sequencing of the 16S rRNA gene was performed for one isolate per cluster. In total, 2500 colonies appeared on the nutrient agar plates, and 244 were purified for further analysis. Good identification was obtained for 202 (83%) isolates by MALDI-TOF MS. The most common genera were Bacillus (n=94, 45%) and Staphyloccocus (n=55, 26%). Poor identification was obtained for 42 (17%) isolates, and their spectra clustering revealed that these isolates belonged to 10 species. Four of these were considered to be new species. CONCLUSIONS During the Hajj, the air was contaminated by many environmental bacterial agents, and MALDI-TOF MS was successfully adapted for their rapid identification.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Didier Raoult
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France.
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Soro-Yao AA, Schumann P, Thonart P, Djè KM, Pukall R. The Use of MALDI-TOF Mass Spectrometry, Ribotyping and Phenotypic Tests to Identify Lactic Acid Bacteria from Fermented Cereal Foods in Abidjan (Côte d'Ivoire). Open Microbiol J 2014; 8:78-86. [PMID: 25279017 PMCID: PMC4181171 DOI: 10.2174/1874285801408010078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein analysis, automated ribotyping, and phenotypic tests (e.g., cell morphology, gas production from glucose, growth and acid production on homofermemtative-heterofermentative differential (HHD) agar medium, sugar fermentation patterns) were used to identify 23 lactic acid bacteria (LAB) isolated from fermented cereal foods available in Abidjan, Côte d'Ivoire. Pediococcus acidilactici (56.5%), Lactobacillus fermentum (30.4%), L. salivarius (4.3%), P. pentosaceus (4.3%) and L. plantarum subsp. plantarum (4.3%) were the species and subspecies identified. Protein based identification was confirmed by automated ribotyping for selected isolates and was similar to that provided by the phenotypic characterization. MALDI-TOF MS protein analysis provided a high level of discrimination among the isolates and could be used for the rapid screening of LAB starter cultures.
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Affiliation(s)
- Amenan A Soro-Yao
- Food Science and Technology Unit, Nangui Abrogoua University, 02 BP 801 Abidjan 02, Côte d’Ivoire
| | - Peter Schumann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Philippe Thonart
- Wallon Center for Industrial Microbiology (CWBI), University of Liège, Bld du Rectorat 29-B40, B 4000 Liège, Belgium
- Wallon Center of Industrial Biology, Bio-industry Unit, Gembloux Agro-BioTech, 5030 Gembloux, Belgium
| | - Koffi M Djè
- Food Science and Technology Unit, Nangui Abrogoua University, 02 BP 801 Abidjan 02, Côte d’Ivoire
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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