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Martuzzi F, Franceschi P, Formaggioni P. Fermented Mare Milk and Its Microorganisms for Human Consumption and Health. Foods 2024; 13:493. [PMID: 38338628 PMCID: PMC10855475 DOI: 10.3390/foods13030493] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Mare milk is consumed by approximatively 30 million people in the world. In countries in Asia and East Europe, mare milk is mainly consumed as source of fermented products, called koumiss, airag or chigee, alcoholic beverages obtained by means of a culture of bacteria and lactose-fermenting yeasts. Recent research concerning mare milk and its derivatives deals mainly with their potential employment for human health. Studies about the isolation and characterization of Lactobacillus spp. and yeasts from koumiss have been aimed at assessing the potential functional properties of these micro-organisms and to find their employment for the industrial processing of mare milk. The aim of this literature review is to summarize recent research about microorganisms in fermented mare milk products and their potential functional properties.
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Affiliation(s)
- Francesca Martuzzi
- Department of Food and Drug Science, University of Parma, Via delle Scienze, 43124 Parma, Italy;
| | - Piero Franceschi
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy;
| | - Paolo Formaggioni
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy;
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2
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Shangpliang HNJ, Tamang JP. Metagenome-assembled genomes for biomarkers of bio-functionalities in Laal dahi, an Indian ethnic fermented milk product. Int J Food Microbiol 2023; 402:110300. [PMID: 37364321 DOI: 10.1016/j.ijfoodmicro.2023.110300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/28/2023]
Abstract
Laal dahi is a sweetened and soft pudding-like fermented milk product of the Eastern regions of India, which has not been studied for its microbial community structures and health promoting functionality in terms of 'omics' approaches. We applied metagenomic and metagenomes-assembled genomes (MAGs) tools to decipher the biomarkers for genes encoding for different health promoting functionalities in laal dahi. Abundance of bacterial domains was observed with negligible presence of eukaryotes and viruses. Bacillota was the most abundant phylum with different bacterial species viz., Enterococcus italicus, Lactococcus raffinolactis, Lactobacillus helveticus, Bifidobacterium mongoliense, Hafnia alvei, Lactococcus lactis, Acetobacter okinawensis, Streptococcus thermophilus, Thermus thermophilus, Leuconostoc citreum, Leuconostoc pseudomesenteroides, Acetobacter orientalis, Lactobacillus gallinarum, Lactococcus chungangensis and Lactobacillus delbrueckii. Comparison of laal dahi microbiome with that of similar fermented milk products was also carried out after retrieving the metagenomic datasets from public databases. Significant abundance of Lb. helveticus, E. italicus, Lc. raffinolactis and Lc. lactis in laal dahi. Interestingly, Bifidobacterium mongoliense, Lb. gallinarum, Lc. chungangensis and Acetobacter okinawensis were only detected in laal dahi but Streptococcus infantarius, Lacticaseibacillus rhamnosus and Lb. johnsonii were absent. Reconstruction of putative single environment-specific genomes from metagenomes in addition to subsampling of the abundant species resulted in five high-quality MAGs identified as Lactobacillus delbrueckii, Lactobacillus helveticus, Lactococcus chungangensis, Lactococcus lactis and Streptococcus thermophilus. All MAGs showed the presence of various genes with several putative functions corresponding to different probiotic and prebiotic functions, short-chain fatty acids production, immunomodulation, antitumor genes, essential amino acid and vitamin biosynthesis. Genes for γ-Aminobutyric acid (GABA) production were only detected in MAG of Lactococcus lactis. Gene clusters for secondary metabolites (antimicrobial peptides) were detected in all MAGs except Lc. chungangensis. Additionally, detection of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) elements was observed only in Lactobacillus delbrueckii and Streptococcus thermophilus. Annotation of several genes with potential health beneficial properties in all five MAGs may support the need to explore the culturability of these MAGs for future use in controlled fermentation of functional dairy products.
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Affiliation(s)
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Tadong, Gangtok 737102, Sikkim, India.
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Kochetkova TV, Grabarnik IP, Klyukina AA, Zayulina KS, Elizarov IM, Shestakova OO, Gavirova LA, Malysheva AD, Shcherbakova PA, Barkhutova DD, Karnachuk OV, Shestakov AI, Elcheninov AG, Kublanov IV. Microbial Communities of Artisanal Fermented Milk Products from Russia. Microorganisms 2022; 10:microorganisms10112140. [PMID: 36363732 PMCID: PMC9697859 DOI: 10.3390/microorganisms10112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia. The examined FMPs were produced from cow, camel, mare’s or mixed milk, in the traditional way, without adding commercial starter cultures. Lactate and acetate were the major volatile fatty acids (VFA) of the studied FMPs, while succinate, formate, propionate and n-butyrate were present in lower concentrations. Bacterial communities analyzed by 16S rRNA gene V4 fragment amplicon sequencing showed that Firmicutes (Lactococcus, Lactobacillus, Streptococcus, Lentilactobacillus and Leuconostoc) was the predominant phylum in all analyzed FMPs, followed by Proteobacteria (Acetobacter, Klebsiella, Pseudomonas and Citrobacter). Lactobacillus (mainly in beverages) or Lactococcus (mainly in creamy and solid products) were the most abundant community-forming genera in FMPs where raw milk was used and fermentation took place at (or below) room temperature. In turn, representatives of Streptococcus genus dominated the FMPs made from melted or pasteurized milk and fermented at elevated temperatures (such as ryazhenka, cottage cheese and matsoni-like products). It was revealed that the microbial diversity of koumiss, shubat, ryazhenka, matsoni-like products, chegen, sour cream and bryndza varied slightly within each type and correlated well with the same products from other regions and countries. On the other hand, the microbiomes of kefir, prostokvasha, ayran, cottage cheese and suluguni-like cheese were more variable and were shaped by the influence of particular factors linked with regional differences and traditions expressed in specificities in the production process. The microbial diversity of aarts, khurunga, khuruud, tan, ayran and suluguni-like cheese was studied here, to our knowledge, for the first time. The results of this study emphasize the overall similarity of the microbial communities of various FMPs on the one hand, and specificities of regional products on the other. The latter are of particular value in the age of globalization when people have begun searching for new and unusual products and properties. Speaking more specifically, these novel products, with their characteristic communities, might be used for the development of novel microbial associations (i.e., starters) to produce novel products with improved or unique properties.
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Affiliation(s)
- Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
- Correspondence:
| | - Ilya P. Grabarnik
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 197101 Saint Petersburg, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | | | - Liliya A. Gavirova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | | | - Darima D. Barkhutova
- Institute of General and Experimental Biology Siberian Branch of the Russian Academy of Sciences, 600047 Ulan-Ude, Russia
| | - Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Andrey I. Shestakov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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Kioukis A, Pourjam M, Neuhaus K, Lagkouvardos I. Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling. FRONTIERS IN BIOINFORMATICS 2022; 2:864597. [PMID: 36304326 PMCID: PMC9580952 DOI: 10.3389/fbinf.2022.864597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial diversity is often analyzed using 16S rRNA gene amplicon sequencing. Commonly, sequences are clustered based on similarity cutoffs to obtain groups reflecting molecular species, genera, or families. Due to the amount of the generated sequencing data, greedy algorithms are preferred for their time efficiency. Such algorithms rely only on pairwise sequence similarities. Thus, sometimes sequences with diverse phylogenetic background are clustered together. In contrast, taxonomic classifiers use position specific taxonomic information in assigning a probable taxonomy to a given sequence. Here we introduce Taxonomy Informed Clustering (TIC), a novel approach that utilizes classifier-assigned taxonomy to restrict clustering to only those sequences that share the same taxonomic path. Based on this concept, we offer a complete and automated pipeline for processing of 16S rRNA amplicon datasets in diversity analyses. First, raw reads are processed to form denoised amplicons. Next, the denoised amplicons are taxonomically classified. Finally, the TIC algorithm progressively assigning clusters at molecular species, genus and family levels. TIC outperforms greedy clustering algorithms like USEARCH and VSEARCH in terms of clusters’ purity and entropy, when using data from the Living Tree Project as test samples. Furthermore, we applied TIC on a dataset containing all Bifidobacteriaceae-classified sequences from the IMNGS database. Here, TIC identified evidence for 1000s of novel molecular genera and species. These results highlight the straightforward application of the TIC pipeline and superior results compared to former methods in diversity studies. The pipeline is freely available at: https://github.com/Lagkouvardos/TIC.
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Affiliation(s)
| | - Mohsen Pourjam
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technical University Munich, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technical University Munich, Freising, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technical University Munich, Freising, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- *Correspondence: Ilias Lagkouvardos,
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5
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Pino A, Benkaddour B, Inturri R, Amico P, Vaccaro SC, Russo N, Vaccalluzzo A, Agolino G, Caggia C, Miloud H, Randazzo CL. Characterization of Bifidobacterium asteroides Isolates. Microorganisms 2022; 10:655. [PMID: 35336230 PMCID: PMC8950671 DOI: 10.3390/microorganisms10030655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Bifidobacteria have long been recognized as bacteria with probiotic and therapeutic features. The aim of this work is to characterize the Bifidobacterium asteroides BA15 and BA17 strains, isolated from honeybee gut, to evaluate its safety for human use. An in-depth assessment was carried out on safety properties (antibiotic resistance profiling, β-hemolytic, DNase and gelatinase activities and virulence factor presence) and other properties (antimicrobial activity, auto-aggregation, co-aggregation and hydrophobicity). Based on phenotypic and genotypic characterization, both strains satisfied all the safety requirements. More specifically, genome analysis showed the absence of genes encoding for glycopeptide (vanA, vanB, vanC-1, vanC-2, vanD, vanE, vanG), resistance to tetracycline (tetM, tetL and tetO) and virulence genes (asa1, gelE, cylA, esp, hyl).
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
| | - Bachir Benkaddour
- Department of Biology, Faculty of Natural Sciences and Life, University of Oran1, Oran 31000, Algeria; (B.B.); (H.M.)
| | - Rosanna Inturri
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Department of R&D, Local Noto Unit, Fidia Farmaceutici S.p.A., 96017 Noto, Italy; (P.A.); (S.C.V.)
| | - Pietro Amico
- Department of R&D, Local Noto Unit, Fidia Farmaceutici S.p.A., 96017 Noto, Italy; (P.A.); (S.C.V.)
| | - Susanna C. Vaccaro
- Department of R&D, Local Noto Unit, Fidia Farmaceutici S.p.A., 96017 Noto, Italy; (P.A.); (S.C.V.)
| | - Nunziatina Russo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
| | - Amanda Vaccalluzzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
| | - Gianluigi Agolino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
| | - Hadadji Miloud
- Department of Biology, Faculty of Natural Sciences and Life, University of Oran1, Oran 31000, Algeria; (B.B.); (H.M.)
| | - Cinzia L. Randazzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
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6
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Alessandri G, van Sinderen D, Ventura M. The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host. Comput Struct Biotechnol J 2021; 19:1472-1487. [PMID: 33777340 PMCID: PMC7979991 DOI: 10.1016/j.csbj.2021.03.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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7
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Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut. Microorganisms 2020; 9:microorganisms9010008. [PMID: 33375064 PMCID: PMC7822027 DOI: 10.3390/microorganisms9010008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host–microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.
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Eckel VPL, Ziegler LM, Vogel RF, Ehrmann M. Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir. Int J Syst Evol Microbiol 2020; 70:1562-1570. [PMID: 31860428 DOI: 10.1099/ijsem.0.003936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Bifidobacterium strains, TMW 2.2057T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium, with Bifidobacterium subtile DSM 20096T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA-DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057T (=DSM 108414T=LMG 31086T) is the type strain.
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Affiliation(s)
- Viktor P L Eckel
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Lisa-Marie Ziegler
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Rudi F Vogel
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Matthias Ehrmann
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
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Wong CB, Odamaki T, Xiao JZ. Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits. FEMS Microbiol Rev 2020; 44:369-385. [PMID: 32319522 PMCID: PMC7326374 DOI: 10.1093/femsre/fuaa010] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Members of Bifidobacterium are among the first microbes to colonise the human gut, and certain species are recognised as the natural resident of human gut microbiota. Their presence in the human gut has been associated with health-promoting benefits and reduced abundance of this genus is linked with several diseases. Bifidobacterial species are assumed to have coevolved with their hosts and include members that are naturally present in the human gut, thus recognised as Human-Residential Bifidobacteria (HRB). The physiological functions of these bacteria and the reasons why they occur in and how they adapt to the human gut are of immense significance. In this review, we provide an overview of the biology of bifidobacteria as members of the human gut microbiota and address factors that contribute to the preponderance of HRB in the human gut. We highlight some of the important genetic attributes and core physiological traits of these bacteria that may explain their adaptive advantages, ecological fitness, and competitiveness in the human gut. This review will help to widen our understanding of one of the most important human commensal bacteria and shed light on the practical consideration for selecting bifidobacterial strains as human probiotics.
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Affiliation(s)
- Chyn Boon Wong
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| | - Jin-zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
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10
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Genomic and physiological insights into the lifestyle of Bifidobacterium species from water kefir. Arch Microbiol 2020; 202:1627-1637. [PMID: 32266422 DOI: 10.1007/s00203-020-01870-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/26/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
Abstract
Water kefir is a fermented beverage employing a natural microbial consortium, which harbours bifidobacteria, namely Bifidobacterium aquikefiri and Bifidobacterium tibiigranuli. However, little information is available on their metabolic properties or role in the consortium. In this study, we combined genomic and physiologic investigations to predict and characterize the properties of these organisms and their possible role in the consortium. When comparing the genomes of these psychrotrophic organisms with that of the three selected mesophilic probiotic Bifidobacterium strains, we could find 143 genes shared by the 3 known isolates of bifidobacteria from water kefir that do not occur in the probiotic strains. These include genes involved in acid and oxygen tolerance. In addition, their genomically predicted carbohydrate usage and transport suggest adaptation to sucrose and other plant-related sugars. Furthermore, they proved prototrophic for all amino acids in vitro, which enables them to cope with the strong amino acid limitation in water kefir.
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11
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Gargari G, Taverniti V, Koirala R, Gardana C, Guglielmetti S. Impact of a Multistrain Probiotic Formulation with High Bifidobacterial Content on the Fecal Bacterial Community and Short-Chain Fatty Acid Levels of Healthy Adults. Microorganisms 2020; 8:microorganisms8040492. [PMID: 32235660 PMCID: PMC7232159 DOI: 10.3390/microorganisms8040492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 02/08/2023] Open
Abstract
The consumption of probiotic products is continually increasing, supported by growing scientific evidence of their efficacy. Considering that probiotics may primarily affect health (either positively or negatively) through gut microbiota modulation, the first aspect that should be evaluated is their impact on the intestinal microbial ecosystem. In this study, we longitudinally analyzed the bacterial taxonomic composition and organic acid levels in four fecal samples collected over the course of four weeks from 19 healthy adults who ingested one capsule a day for two weeks of a formulation containing at least 70 billion colony-forming units, consisting of 25% lactobacilli and 75% Bifidobacterium animalis subsp. lactis. We found that 16S rRNA gene profiling showed that probiotic intake only induced an increase in a single operational taxonomic unit ascribed to B. animalis, plausibly corresponding to the ingested bifidobacterial strain. Furthermore, liquid chromatography/mass spectrometry revealed a significant increase in the lactate and acetate/butyrate ratio and a trend toward a decrease in succinate following probiotic administration. The presented results indicate that the investigated probiotic formulation did not alter the intestinal bacterial ecosystem of healthy adults and suggest its potential ability to promote colonization resistance in the gut through a transient increase in fecal bifidobacteria, lactic acid, and the acetate/butyrate ratio.
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Affiliation(s)
- Giorgio Gargari
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
| | - Valentina Taverniti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
| | - Ranjan Koirala
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
| | - Claudio Gardana
- Division of Human Nutrition, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy;
| | - Simone Guglielmetti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
- Correspondence: ; Tel.: +39-02-5031-9136
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12
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Gao J, Azad MAK, Han H, Wan D, Li T. Impact of Prebiotics on Enteric Diseases and Oxidative Stress. Curr Pharm Des 2020; 26:2630-2641. [PMID: 32066357 DOI: 10.2174/1381612826666200211121916] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022]
Abstract
In animals, the gastrointestinal microbiota are reported to play a major role in digestion, nutrient absorption and the release of energy through metabolism of food. Therefore, microbiota may be a factor for association between diet and enteric diseases and oxidative stress. The gut microbial composition and concentration are affected by diet throughout the life of an animal, and respond rapidly and efficiently to dietary alterations, in particular to the use of prebiotics. Prebiotics, which play an important role in mammalian nutrition, are defined as dietary ingredients that lead to specific changes in both the composition and activity of the gastrointestinal microbiota through suppressing the proliferation of pathogens and by modifying the growth of beneficial microorganisms in the host intestine. A review of the evidence suggests possible beneficial effects of prebiotics on host intestinal health, including immune stimulation, gut barrier enhancement and the alteration of the gastrointestinal microbiota, and these effects appear to be dependent on alteration of the bacterial composition and short-chain fatty acid (SCFA) production. The production of SCFAs depends on the microbes available in the gut and the type of prebiotics available. The SCFAs most abundantly generated by gastrointestinal microbiota are acetate, butyrate and propionate, which are reported to have physiological effects on the health of the host. Nowadays, prebiotics are widely used in a range of food products to improve the intestinal microbiome and stimulate significant changes to the immune system. Thus, a diet with prebiotic supplements may help prevent enteric disease and oxidative stress by promoting a microbiome associated with better growth performance. This paper provides an overview of the hypothesis that a combination of ingestible prebiotics, chitosan, fructooligosaccharides and inulin will help relieve the dysbiosis of the gut and the oxidative stress of the host.
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Affiliation(s)
- Jing Gao
- Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha, Hunan, China,Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China,National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production,
Changsha, Hunan 410125, China,University of Chinese Academy of Sciences, Beijing, China
| | - Md A K Azad
- Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha, Hunan, China,Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China,National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production,
Changsha, Hunan 410125, China,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Han
- Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha, Hunan, China,Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China,National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production,
Changsha, Hunan 410125, China,University of Chinese Academy of Sciences, Beijing, China
| | - Dan Wan
- Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha, Hunan, China,Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China,National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production,
Changsha, Hunan 410125, China,University of Chinese Academy of Sciences, Beijing, China
| | - TieJun Li
- Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha, Hunan, China,Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China,National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production,
Changsha, Hunan 410125, China,University of Chinese Academy of Sciences, Beijing, China
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13
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Tamang JP, Cotter PD, Endo A, Han NS, Kort R, Liu SQ, Mayo B, Westerik N, Hutkins R. Fermented foods in a global age: East meets West. Compr Rev Food Sci Food Saf 2020; 19:184-217. [PMID: 33319517 DOI: 10.1111/1541-4337.12520] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Abstract
Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.
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Affiliation(s)
- Jyoti Prakash Tamang
- DAICENTER and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Paul D Cotter
- Food Biosciences, Principal Research Officer, Teagasc Food Research Centre, Moorepark, Fermoy and APC Microbiome Ireland, Cork, Ireland
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Tokyo, Japan
| | - Nam Soo Han
- Department of Food Science and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Remco Kort
- Department of Molecular Cell Biology, VU University Amsterdam, The Netherlands.,Yoba for Life foundation, Amsterdam, The Netherlands
| | - Shao Quan Liu
- Food Science and Technology Programme, National University of Singapore
| | - Baltasar Mayo
- Department of Microbiology and Chemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Nieke Westerik
- Department of Molecular Cell Biology, VU University Amsterdam, The Netherlands.,Yoba for Life foundation, Amsterdam, The Netherlands
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska
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14
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Bifidobacterial Distribution Across Italian Cheeses Produced from Raw Milk. Microorganisms 2019; 7:microorganisms7120599. [PMID: 31766566 PMCID: PMC6955966 DOI: 10.3390/microorganisms7120599] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/06/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022] Open
Abstract
Cheese microbiota is of high industrial relevance due to its crucial role in defining the organoleptic features of the final product. Nevertheless, the composition of and possible microbe-microbe interactions between these bacterial populations have never been assessed down to the species-level. For this reason, 16S rRNA gene microbial profiling combined with internally transcribed spacer (ITS)-mediated bifidobacterial profiling analyses of various cheeses produced with raw milk were performed in order to achieve an in-depth view of the bifidobacterial populations present in these microbially fermented food matrices. Moreover, statistical elaboration of the data collected in this study revealed the existence of community state types characterized by the dominance of specific microbial genera that appear to shape the overall cheese microbiota through an interactive network responsible for species-specific modulatory effects on the bifidobacterial population.
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15
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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16
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Arzamasov AA, van Sinderen D, Rodionov DA. Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization. Front Microbiol 2018; 9:776. [PMID: 29740413 PMCID: PMC5928203 DOI: 10.3389/fmicb.2018.00776] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/05/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Bifidobacterium are common inhabitants of the human gastrointestinal tract. Previously it was shown that arabino-oligosaccharides (AOS) might act as prebiotics and stimulate the bifidobacterial growth in the gut. However, despite the rapid accumulation of genomic data, the precise mechanisms by which these sugars are utilized and associated transcription control still remain unclear. In the current study, we used a comparative genomic approach to reconstruct arabinose and AOS utilization pathways in over 40 bacterial species belonging to the Bifidobacteriaceae family. The results indicate that the gene repertoire involved in the catabolism of these sugars is highly diverse, and even phylogenetically close species may differ in their utilization capabilities. Using bioinformatics analysis we identified potential DNA-binding motifs and reconstructed putative regulons for the arabinose and AOS utilization genes in the Bifidobacteriaceae genomes. Six LacI-family transcriptional factors (named AbfR, AauR, AauU1, AauU2, BauR1 and BauR2) and a TetR-family regulator (XsaR) presumably act as local repressors for AOS utilization genes encoding various α- or β-L-arabinofuranosidases and predicted AOS transporters. The ROK-family regulator AraU and the LacI-family regulator AraQ control adjacent operons encoding putative arabinose transporters and catabolic enzymes, respectively. However, the AraQ regulator is universally present in all Bifidobacterium species including those lacking the arabinose catabolic genes araBDA, suggesting its control of other genes. Comparative genomic analyses of prospective AraQ-binding sites allowed the reconstruction of AraQ regulons and a proposed binary repression/activation mechanism. The conserved core of reconstructed AraQ regulons in bifidobacteria includes araBDA, as well as genes from the central glycolytic and fermentation pathways (pyk, eno, gap, tkt, tal, galM, ldh). The current study expands the range of genes involved in bifidobacterial arabinose/AOS utilization and demonstrates considerable variations in associated metabolic pathways and regulons. Detailed comparative and phylogenetic analyses allowed us to hypothesize how the identified reconstructed regulons evolved in bifidobacteria. Our findings may help to improve carbohydrate catabolic phenotype prediction and metabolic modeling, while it may also facilitate rational development of novel prebiotics.
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Affiliation(s)
- Aleksandr A Arzamasov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College Cork, Cork, Ireland
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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17
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Modesto M, Michelini S, Sansosti MC, De Filippo C, Cavalieri D, Qvirist L, Andlid T, Spiezio C, Sandri C, Pascarelli S, Sgorbati B, Mattarelli P. Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 68:141-148. [PMID: 29116036 DOI: 10.1099/ijsem.0.002472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (Saguinus imperator). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5T was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5T was closely related to Bifidobacterium saguini DSM 23967T (96.4 %) and to Bifidobacterium longum subsp. longum ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to Bifidobacterium breve DSM 20213T (hsp60 94.1 %), Bifidobacterium saguini DSM 23967T (clpC 91 %), Bifidobacterium avesanii DSM 100685T (dnaG 80.3 %), Bifidobacterium longumsubsp. infantis ATCC 15697T (dnaJ 85.3 %) and Bifidobacterium longumsubsp. longum ATCC 15708 (rpoB 93 %), respectively. The peptidoglycan type was A3β, with an interpeptide bridge comprising l-Orn (Lys) - l-Ser - l-Ala - l-Thr - l-Ala. The DNA G+C content of strain TRI 5T was 60.9 mol%. Based on the data provided, strain TRI 5T represents a novel species of the genus Bifidobacterium for which the name Bifidobacteriumcallitrichidarum sp. nov. is proposed. The type strain is TRI 5T (=DSM 103152T=JCM 31790T).
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Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza della Manifattura 1, 38068 Rovereto (TN), Italy
| | - Maria Cristina Sansosti
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Moruzzi, 156124 Pisa, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Linnea Qvirist
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Thomas Andlid
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Caterina Spiezio
- Parco Natura Viva Garda Zoological Park S.r.l, Località Figara 40, 37012 Bussolengo (VR), Italy
| | - Camillo Sandri
- Parco Natura Viva Garda Zoological Park S.r.l, Località Figara 40, 37012 Bussolengo (VR), Italy
| | - Stefano Pascarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.,Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Barbara Sgorbati
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.,School of Pharmacy, Biotechnology and Sport Science, Viale Berti Pichat 10, 40100 Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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18
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Nomoto R, Takano S, Tanaka K, Tsujikawa Y, Kusunoki H, Osawa R. Isolation and identification of Bifidobacterium species from feces of captive chimpanzees. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2017; 36:91-99. [PMID: 28748130 PMCID: PMC5510154 DOI: 10.12938/bmfh.16-027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022]
Abstract
Recently, gut-dwelling bifidobacteria from chimpanzees, which are phylogenetically close to humans and have feeding habits similar to humans, have been frequently investigated. Given this, we speculated that like humans,
chimpanzees would have a unique diversity of bifidobacteria. We herein describe a taxonomically novel member of bifidobacteria isolated from fecal samples of captive chimpanzees. Bifidobacteria were detected in all fecal samples
by quantitative polymerase chain reaction. A Bifidobacterium pseudolongum-like species, which could not be detected using B. pseudolongum-specific primers targeting the groEL gene
sequence, was dominant in the feces of five chimpanzees. Seven bifidobacterial strains were isolated from this group of five chimpanzees, and all isolates were identified as B. pseudolongum. B.
pseudolongum has previously often been isolated from non-primate animals as well as humans; however, here we demonstrate its presence in a nonhuman primate species.
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Affiliation(s)
- Ryohei Nomoto
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan.,Health Bioscience Team, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Shintaro Takano
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Kosei Tanaka
- Health Bioscience Team, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Yuji Tsujikawa
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Hiroshi Kusunoki
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Ro Osawa
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan.,Health Bioscience Team, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
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19
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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: 335] [Impact Index Per Article: 41.9] [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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20
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Laureys D, Cnockaert M, De Vuyst L, Vandamme P. Bifidobacterium aquikefiri sp. nov., isolated from water kefir. Int J Syst Evol Microbiol 2016; 66:1281-1286. [PMID: 26739269 DOI: 10.1099/ijsem.0.000877] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Bifidobacterium, strain LMG 28769T, was isolated from a household water kefir fermentation process. Cells were Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, oxidase-negative and facultatively anaerobic short rods. Analysis of its 16S rRNA gene sequence revealed Bifidobacterium crudilactis and Bifidobacterium psychraerophilum (97.4 and 97.1 % similarity towards the respective type strain sequences) as nearest phylogenetic neighbours. Its assignment to the genus Bifidobacterium was confirmed by the presence of fructose 6-phosphate phosphoketolase activity. Analysis of the hsp60 gene sequence revealed very low similarity with nucleotide sequences in the NCBI nucleotide database. The genotypic and phenotypic analyses allowed the differentiation of strain LMG 28769T from all recognized Bifidobacterium species. Strain LMG 28769T ( = CCUG 67145T = R 54638T) therefore represents a novel species, for which the name Bifidobacterium aquikefiri sp. nov. is proposed.
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Affiliation(s)
- David Laureys
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University,K. L., Ledeganckstraat 35, B-9000 Ghent,Belgium.,Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel,Pleinlaan 2, B-1050, Brussels,Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University,K. L., Ledeganckstraat 35, B-9000 Ghent,Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel,Pleinlaan 2, B-1050, Brussels,Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University,K. L., Ledeganckstraat 35, B-9000 Ghent,Belgium
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21
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Bunesova V, Vlkova E, Rada V, Killer J, Musilova S. Bifidobacteria from the gastrointestinal tract of animals: differences and similarities. Benef Microbes 2015; 5:377-88. [PMID: 24889892 DOI: 10.3920/bm2013.0081] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
At present, the genus Bifidobacterium includes 48 species and subspecies, and this number is expected to increase. Bifidobacteria are found in different ecological niches. However, most were originally isolated from animals, mainly mammals, especially during the milk feeding period of life. Their presence in high numbers is associated with good health of the host. Moreover, bifidobacteria are often found in poultry and insects that exhibit a social mode of life (honeybees and bumblebees). This review is designed as a summary of currently known species of the genus Bifidobacterium, especially focused on their difference and similarities. The primary focus is on their occurrence in the digestive tract of animals, as well as the specificities of animal strains, with regard to their potential use as probiotics.
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Affiliation(s)
- V Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
| | - E Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
| | - V Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
| | - J Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14200 Prague 4-Krč, Czech Republic
| | - S Musilova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 16521 Prague 6-Suchdol, Czech Republic
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22
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Yanokura E, Oki K, Makino H, Modesto M, Pot B, Mattarelli P, Biavati B, Watanabe K. Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets. Syst Appl Microbiol 2015; 38:305-14. [PMID: 26007614 DOI: 10.1016/j.syapm.2015.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/30/2015] [Accepted: 05/06/2015] [Indexed: 11/28/2022]
Abstract
The species Bifidobacterium longum is currently divided into three subspecies, B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. This classification was based on an assessment of accumulated information on the species' phenotypic and genotypic features. The three subspecies of B. longum were investigated using genotypic identification [amplified-fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST)]. By using the AFLP and the MLSA methods, we allocated 25 strains of B. longum into three major clusters corresponding to the three subspecies; the cluster comprising the strains of B. longum subsp. suis was further divided into two subclusters differentiable by the ability to produce urease. By using the MLST method, the 25 strains of B. longum were divided into eight groups: four major groups corresponding to the results obtained by AFLP and MLSA, plus four minor disparate groups. The results of AFLP, MLSA and MLST analyses were consistent and revealed a novel subspeciation of B. longum, which comprised three known subspecies and a novel subspecies of urease-negative B. longum, for which the name B. longum subsp. suillum subsp. nov. is proposed, with type strain Su 851(T)=DSM 28597(T)=JCM 19995(T).
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Affiliation(s)
- Emiko Yanokura
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan
| | - Kaihei Oki
- Yakult Honsha European Research Center for Microbiology ESV, Technologiepark 4, 9052 Zwijnaarde, Belgium
| | - Hiroshi Makino
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Bruno Pot
- Lactic acid Bacteria and Mucosal Immunity Team, Institut Pasteur de Lille, Rue Prof. Calmette, F-59019 Lille Cedex, France; Center for Infection and Immunity of Lille, F-59019 Lille, France; Université Lille Nord de France, F-59019 Lille, France; CNRS, UMR 8204, F-59019 Lille, France
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Bruno Biavati
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec 3, Keelung Rd., Taipei 10673, Taiwan, ROC.
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Wang F, Huang G, Cai D, Li D, Liang X, Yu T, Shen P, Su H, Liu J, Gu H, Zhao M, Li Q. Qualitative and Semiquantitative Analysis of Fecal Bifidobacterium Species in Centenarians Living in Bama, Guangxi, China. Curr Microbiol 2015; 71:143-9. [PMID: 26003628 DOI: 10.1007/s00284-015-0804-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/24/2015] [Indexed: 12/27/2022]
Abstract
Centenarians constitute a significant subpopulation in the Bama County of Guangxi province in China. The beneficial effects of intestinal microbiota, especially bifidobacteria of centenarians, have been widely accepted; however, knowledge about Bifidobacterium species in centenarians is not adequate. The aim of this study was to investigate the quantity and prevalence of fecal Bifidobacterium in healthy longevous individuals. Fecal samples from eight centenarians from Bama (aged 100 to 108 years), eight younger elderlies from Bama (aged 80 to 99 years), and eight younger elderlies from Nanning (aged 80 to 99 years) were analyzed using denaturing gradient gel electrophoresis, species-specific clone library, and quantitative polymerase chain reaction technology (qPCR). A total of eight different Bifidobacterium species were detected. B. dentium, B. longum, B. thermophilum, B. pseudocatenulatum/B. catenulatum, and B. adolescentis were common in fecal of centenarians and young elderly. B. minimum, B. saecularmay/B. pullorum/B. gallinarum, and B. mongoliense were found in centenarians but were absent in the younger elderlies. In addition, Bifidobacterium species found in centenarians were different from those found in Bama young elderly and Nanning young elderly, and the principal differences were the significant increase in the population of B. longum (P < 0.05) and B. dentium (P < 0.05) and the reduction in the frequency of B. adolescentis (P < 0.05), respectively. Centenarians tend to have more complex fecal Bifidobacterium species than young elderlies from different regions.
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Affiliation(s)
- Fang Wang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, 530004, People's Republic of China
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24
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Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C, Pisi A, Filippini G, Biavati B, Mattarelli P. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta). Int J Syst Evol Microbiol 2015; 65:1726-1734. [PMID: 25736415 DOI: 10.1099/ijs.0.000162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from a faecal sample of a 5-year-old ring-tailed lemur (Lemur catta). The strains showed a peculiar morphology, resembling a small coiled snake, a ring shape, or forming a little 'Y' shape. The isolated strains appeared identical, and LMC 13T was chosen as a representative strain and characterized further. Strain LMC 13T showed an A3β peptidoglycan type, similar to that found in Bifidobacterium longum. The DNA base composition was 57.2 mol% G+C. Almost-complete 16S rRNA, hsp60, rpoB, dnaJ, dnaG, purF, clpC and rpoC gene sequences were obtained, and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strain LMC 13T showed the highest similarity to B. longum subsp. suis ATCC 27533T (96.65 %) and Bifidobacterium saguini DSM 23967T (96.64 %). Strain LMC 13T was located in an actinobacterial cluster and was more closely related to the genus Bifidobacteriumthan to other genera in the Bifidobacteriaceae. On the basis of these results, strain LMC 13T represents a novel species within the genus Bifidobacterium, for which the name Bifidobacterium lemurum sp. nov. is proposed; the type strain is LMC 13T ( = DSM 28807T = JCM 30168T).
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Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Ilaria Stefanini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Camillo Sandri
- Natura Viva Garda Zoological Park S.r.l, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Natura Viva Garda Zoological Park S.r.l, Bussolengo, Verona, Italy
| | - Annamaria Pisi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | | | - Bruno Biavati
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
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25
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Ringø E, Andersen R, Sperstad S, Zhou Z, Ren P, Breines EM, Hareide E, Yttergård GJ, Opsal K, Johansen HM, Andreassen AK, Kousha A, Godfroid J, Holzapfel W. Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods. FOOD BIOTECHNOL 2014. [DOI: 10.1080/08905436.2014.964253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Kimoto-Nira H, Yamasaki S, Sasaki K, Moriya N, Takenaka A, Suzuki C. New lactic acid bacterial strains from traditional Mongolian fermented milk products have altered adhesion to porcine gastric mucin depending on the carbon source. Anim Sci J 2014; 86:325-32. [PMID: 25186082 DOI: 10.1111/asj.12270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/04/2014] [Indexed: 11/30/2022]
Abstract
Attachment of lactic acid bacteria to the mucosal surface of the gastrointestinal tract is a major property of probiotics. Here, we examined the ability of 21 lactic acid bacterial strains isolated from traditional fermented milk products in Mongolia to adhere to porcine gastric mucin in vitro. Higher attachment was observed with Lactobacillus delbrueckii subsp. bulgaricus strains 6-8 and 8-1 than with Lactobacillus rhamnosus GG (positive control). Lactococcus lactis subsp. cremoris strain 7-1 adhered to mucin as effectively as did strain GG. Heat inactivation decreased the adhesive ability of strains 6-8 and 8-1 but did not affect strain 7-1. The adhesion of strains 6-8, 7-1 and 8-1 was significantly inhibited when the cells were pretreated with periodate and trypsin, indicating that proteinaceous and carbohydrate-like cell surface compounds are involved in the adhesion of these strains. The adhesion of strain 7-1 was affected by the type of carbohydrate present in the growth medium, being higher with fructose than with lactose, galactose or xylose as the carbon source. The sugar content of 7-1 cells grown on various carbohydrates was negatively correlated with its adhesive ability. We provide new probiotic candidate strains and new information regarding carbohydrate preference that influences lactic acid bacterial adhesion to mucin.
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27
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Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M. Diversity, ecology and intestinal function of bifidobacteria. Microb Cell Fact 2014; 13 Suppl 1:S4. [PMID: 25186128 PMCID: PMC4155821 DOI: 10.1186/1475-2859-13-s1-s4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The human gastrointestinal tract represents an environment which is a densely populated home for a microbiota that has evolved to positively contribute to host health. At birth the essentially sterile gastrointestinal tract (GIT) is rapidly colonized by microorganisms that originate from the mother and the surrounding environment. Within a short timeframe a microbiota establishes within the (breastfed) infant's GIT where bifidobacteria are among the dominant members, although their numerical dominance disappears following weaning. The numerous health benefits associated with bifidobacteria, and the consequent commercial relevance resulting from their incorporation into functional foods, has led to intensified research aimed at the molecular understanding of claimed probiotic attributes of this genus. In this review we provide the current status on the diversity and ecology of bifidobacteria. In addition, we will discuss the molecular mechanisms that allow this intriguing group of bacteria to colonize and persist in the GIT, so as to facilitate interaction with its host.
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28
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Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Appl Environ Microbiol 2014; 80:6383-94. [PMID: 25107967 DOI: 10.1128/aem.02004-14] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bifidobacterium genus currently encompasses 48 recognized taxa, which have been isolated from different ecosystems. However, the current phylogeny of bifidobacteria is hampered by the relative paucity of genotypic data. Here, we reassessed the taxonomy of this bacterial genus using genome-based approaches, which demonstrated that the previous taxonomic view of bifidobacteria contained several inconsistencies. In particular, high levels of genetic relatedness were shown to exist between particular Bifidobacterium taxa which would not justify their status as separate species. The results presented are here based on average nucleotide identity analysis involving the genome sequences for each type strain of the 48 bifidobacterial taxa, as well as phylogenetic comparative analysis of the predicted core genome of the Bifidobacterium genus. The results of this study demonstrate that the availability of complete genome sequences allows the reconstruction of a more robust bifidobacterial phylogeny than that obtained from a single gene-based sequence comparison, thus discouraging the assignment of a new or separate bifidobacterial taxon without such a genome-based validation.
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29
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Bunesova V, Killer J, Vlkova E, Musilova S, Tomaska M, Rada V, Kmet V. Isolation and characterization of bifidobacteria from ovine cheese. Int J Food Microbiol 2014; 188:26-30. [PMID: 25086349 DOI: 10.1016/j.ijfoodmicro.2014.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/21/2014] [Accepted: 07/01/2014] [Indexed: 11/18/2022]
Abstract
Animal products are one of the niches of bifidobacteria, a fact probably attributable to secondary contamination. In this study, 2 species of the genus Bifidobacterium were isolated by culture-dependent methods from ovine cheeses that were made from unpasteurized milk without addition of starter cultures. The isolates were identified as Bifidobacterium crudilactis and Bifidobacterium animalis subsp. lactis using matrix-assisted laser desorption/ionization time-of-flight analysis and sequencing of phylogenetic markers (16S rRNA, hsp60, and fusA).
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Affiliation(s)
- Vera Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic.
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic; Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4-Krč 14 200, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Sarka Musilova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Martin Tomaska
- Dairy Research Institute, Dlhá 95, 010 01 Žilina, Slovakia
| | - Vojtech Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Vladimir Kmet
- Institute of Animal Physiology of Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
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30
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Choi JH, Lee KM, Lee MK, Cha CJ, Kim GB. Bifidobacterium faecale sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2014; 64:3134-3139. [PMID: 24944342 DOI: 10.1099/ijs.0.063479-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated strain CU3-7(T), was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7(T) was phylogenetically affiliated with members of the genus Bifidobacterium. Strain CU3-7(T) showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216(T) (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425(T) (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7(T) was closely related to B. adolescentis KCTC 3216(T) (94.0 %) and B. ruminantium KCTC 3425(T) (92.5 %). The DNA-DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425(T) and 14.9 % with B. adolescentis KCTC 3216(T). Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7(T) should be classified as the type strain of a novel species within the genus Bifidobacterium, for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904(T) = JCM 19861(T)).
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Affiliation(s)
- Jung-Hye Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Kyung Min Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Myung-Ki Lee
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam 463-746, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Geun-Bae Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea
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31
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Modesto M, Michelini S, Stefanini I, Ferrara A, Tacconi S, Biavati B, Mattarelli P. Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2014; 64:2819-2827. [PMID: 24867172 DOI: 10.1099/ijs.0.056937-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (Callithrix jacchus). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a 'Y' shape. Strains MRM 3/1(T) and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1(T) showed a peptidoglycan type unique among members of the genus Bifidobacterium. The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, hsp60, clpC and rpoB gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1(T) and MRM 4/2 had the highest similarities to Bifidobacterium scardovii DSM 13734(T) (94.6%) and Bifidobacterium stellenboschense DSM 23968(T) (94.5%). Analysis of hsp60 showed that both strains were closely related to B. stellenboschense DSM 23968(T) (97.5% similarity); however, despite this high degree of similarity, our isolates could be distinguished from B. stellenboschense DSM 23968(T) by low levels of DNA-DNA relatedness (30.4% with MRM 3/1(T)). Strains MRM 3/1(T) and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus Bifidobacterium than to other genera in the family Bifidobacteriaceae. On the basis of these results, strains MRM 3/1(T) and MRM 4/2 represent a novel species within the genus Bifidobacterium, for which the name Bifidobacterium aesculapii sp. nov. is proposed; the type strain is MRM 3/1(T) ( = DSM 26737(T) = JCM 18761(T)).
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Affiliation(s)
- M Modesto
- Department of Agricultural Sciences, University of Bologna, Italy
| | - S Michelini
- Department of Agricultural Sciences, University of Bologna, Italy
| | - I Stefanini
- Department of Agricultural Sciences, University of Bologna, Italy
| | | | | | - B Biavati
- Department of Agricultural Sciences, University of Bologna, Italy
| | - P Mattarelli
- Department of Agricultural Sciences, University of Bologna, Italy
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32
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Oki K, Dugersuren J, Demberel S, Watanabe K. Pyrosequencing analysis of the microbial diversity of airag, khoormog and tarag, traditional fermented dairy products of mongolia. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2014; 33:53-64. [PMID: 25003019 PMCID: PMC4081183 DOI: 10.12938/bmfh.33.53] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/29/2013] [Indexed: 11/05/2022]
Abstract
Here, we used pyrosequencing to obtain a detailed analysis of the microbial diversities of traditional fermented dairy products of Mongolia. From 22 Airag (fermented mare's milk), 5 Khoormog (fermented camel's milk) and 26 Tarag (fermented milk of cows, goats and yaks) samples collected in the Mongolian provinces of Arhangai, Bulgan, Dundgobi, Tov, Uburhangai and Umnugobi, we obtained a total of 81 operational taxonomic units, which were assigned to 15 families, 21 genera and 41 species in 3 phyla. The genus Lactobacillus is a core bacterial component of Mongolian fermented milks, and Lactobacillus helveticus, Lactobacillus kefiranofaciens and Lactobacillus delbrueckii were the predominant species of lactic acid bacteria (LAB) in the Airag, Khoormog and Tarag samples, respectively. By using this pyrosequencing approach, we successfully detected most LAB species that have been isolated as well as seven LAB species that have not been found in our previous culture-based study. A subsequent analysis of the principal components of the samples revealed that L. delbrueckii, L. helveticus, L. kefiranofaciens and Streptococcus thermophilus were the main factors influencing the microbial diversity of these Mongolian traditional fermented dairy products and that this diversity correlated with the animal species from which the milk was sourced.
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Affiliation(s)
- Kaihei Oki
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
| | - Jamyan Dugersuren
- Institute of Veterinary Medicine, Mongolian State University of Agriculture, Zaisan 53, IVM, Ulaanbaatar 17024, Mongolia
| | - Shirchin Demberel
- Institute of Veterinary Medicine, Mongolian State University of Agriculture, Zaisan 53, IVM, Ulaanbaatar 17024, Mongolia
| | - Koichi Watanabe
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan
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33
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Makino H, Kushiro A, Ishikawa E, Kubota H, Gawad A, Sakai T, Oishi K, Martin R, Ben-Amor K, Knol J, Tanaka R. Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota. PLoS One 2013; 8:e78331. [PMID: 24244304 PMCID: PMC3828338 DOI: 10.1371/journal.pone.0078331] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/11/2013] [Indexed: 01/09/2023] Open
Abstract
Objectives Bifidobacterium species are one of the major components of the infant's intestine microbiota. Colonization with bifidobacteria in early infancy is suggested to be important for health in later life. However, information remains limited regarding the source of these microbes. Here, we investigated whether specific strains of bifidobacteria in the maternal intestinal flora are transmitted to their infant's intestine. Materials and Methods Fecal samples were collected from healthy 17 mother and infant pairs (Vaginal delivery: 12; Cesarean section delivery: 5). Mother's feces were collected twice before delivery. Infant's feces were collected at 0 (meconium), 3, 7, 30, 90 days after birth. Bifidobacteria isolated from feces were genotyped by multilocus sequencing typing, and the transitions of bifidobacteria counts in infant's feces were analyzed by quantitative real-time PCR. Results Stains belonging to Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum subsp. longum, and Bifidobacterium pseudocatenulatum, were identified to be monophyletic between mother's and infant's intestine. Eleven out of 12 vaginal delivered infants carried at least one monophyletic strain. The bifidobacterial counts of the species to which the monophyletic strains belong, increased predominantly in the infant's intestine within 3 days after birth. Among infants delivered by C-section, monophyletic strains were not observed. Moreover, the bifidobacterial counts were significantly lower than the vaginal delivered infants until 7 days of age. Conclusions Among infants born vaginally, several Bifidobacterium strains transmit from the mother and colonize the infant's intestine shortly after birth. Our data suggest that the mother's intestine is an important source for the vaginal delivered infant's intestinal microbiota.
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Affiliation(s)
- Hiroshi Makino
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
- * E-mail:
| | - Akira Kushiro
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
| | - Eiji Ishikawa
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
| | - Hiroyuki Kubota
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
- Yakult Honsha European Research Center for Microbiology, ESV, Gent-Zwijnaarde, Belgium
| | - Agata Gawad
- Yakult Honsha European Research Center for Microbiology, ESV, Gent-Zwijnaarde, Belgium
| | - Takafumi Sakai
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
| | - Kenji Oishi
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
- Yakult Honsha European Research Center for Microbiology, ESV, Gent-Zwijnaarde, Belgium
| | - Rocio Martin
- Danone Research, Centre for Specialised Nutrition, Utrecht, The Netherlands
| | | | - Jan Knol
- Danone Research, Centre for Specialised Nutrition, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ryuichiro Tanaka
- Yakult Central Institute for Microbiological Research, Tokyo, Japan
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34
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Delcenserie V, Taminiau B, Gavini F, de Schaetzen MA, Cleenwerck I, Theves M, Mahieu M, Daube G. Detection and characterization of Bifidobacterium crudilactis and B. mongoliense able to grow during the manufacturing process of French raw milk cheeses. BMC Microbiol 2013; 13:239. [PMID: 24164698 PMCID: PMC4231354 DOI: 10.1186/1471-2180-13-239] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 10/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study of a production chain of raw milk cheeses (St Marcellin, Vercors area, France) led to the isolation of two Bifidobacterium populations: B. crudilactis and B. mongoliense, that were able to grow along the production chain. The aims of this study were to further detect and characterize these bacteria along the process and evaluate the ability of some strains to survive or grow in adverse conditions. RESULTS Using PCR coupled with restriction fragment length polymorphism, B. crudilactis and B. mongoliense were detected in respectively 77% and 30% of St Marcellin cheeses from production chain after 21 days of ripening. They were present in more than half of all analyzed retail cheeses with counts going from 1.6 to 5 log cfu g-1 for B. crudilactis and 1.4 to 7 log cfu g-1 for B. mongoliense. Bifidobacterium mongoliense was sensitive to pH 2, with an observed decrease of at least 3 log for both studied strains (FR49/f/2 and FR41/2) after 1 h incubation. At pH 3, no significant decrease was observed. Good survival was observed for the same strains in presence of pancreatic juice with a decrease of less than one log. Survival of strain FR49/f/2 was better than FR41/2 with a decrease of 3 logarithms (in presence of 1% bile salts) and almost 2 logarithms (in presence of 0.5% bile salts). The genotypic analyses using total DNA-DNA hybridization, GC% content, 16S rRNA gene sequencing and multilocus sequencing analysis (MLSA) confirmed the classification of Bifidobacterium. crudilactis and B. mongoliense into two different clusters well separated from other bifidobacteria clusters. CONCLUSIONS According to the observed characteristics such as survival in adverse conditions and their ability to grow under 12 °C during the manufacturing process of the cheeses, which has never been described for bifidobacteria and which is a very interesting technological asset, these B. crudilactis and B. mongoliense strains should be further investigated for a potential use in new food or in food supplements.
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Affiliation(s)
- Veronique Delcenserie
- Food Sciences Department, Faculty of Veterinary Medicine, University of Liège, Sart Tilman, B43b, B-4000 Liege, Belgium.
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Bolado-Martínez E, Acedo-Félix E, Peregrino-Uriarte AB, Yepiz-Plascencia G. Fructose 6-phosphate phosphoketolase activity in wild-type strains of Lactobacillus, isolated from the intestinal tract of pigs. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s000368381205002x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hsieh HH, Wang SY, Chen TL, Huang YL, Chen MJ. Effects of cow's and goat's milk as fermentation media on the microbial ecology of sugary kefir grains. Int J Food Microbiol 2012; 157:73-81. [DOI: 10.1016/j.ijfoodmicro.2012.04.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/28/2012] [Accepted: 04/16/2012] [Indexed: 10/28/2022]
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Metabolic activities and probiotic potential of bifidobacteria. Int J Food Microbiol 2011; 149:88-105. [DOI: 10.1016/j.ijfoodmicro.2011.06.003] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 02/06/2023]
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Delcenserie V, Gavini F, China B, Daube G. Bifidobacterium pseudolongum are efficient indicators of animal fecal contamination in raw milk cheese industry. BMC Microbiol 2011; 11:178. [PMID: 21816092 PMCID: PMC3166927 DOI: 10.1186/1471-2180-11-178] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 08/04/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The contamination of raw milk cheeses (St-Marcellin and Brie) from two plants in France was studied at several steps of production (raw milk, after addition of rennet - St-Marcellin - or after second maturation - Brie -, after removal from the mold and during ripening) using bifidobacteria as indicators of fecal contamination. RESULTS Bifidobacterium semi-quantitative counts were compared using PCR-RFLP and real-time PCR. B. pseudolongum were detected in 77% (PCR-RFLP; 1.75 to 2.29 log cfu ml(-1)) and 68% (real-time PCR; 2.19 to 2.73 log cfu ml(-1)) of St-Marcellin samples and in 87% (PCR-RFLP; 1.17 to 2.40 log cfu ml(-1)) of Brie cheeses samples. Mean counts of B. pseudolongum remained stable along both processes. Two other populations of bifidobacteria were detected during the ripening stage of St-Marcellin, respectively in 61% and 18% of the samples (PCR-RFLP). The presence of these populations explains the increase in total bifidobacteria observed during ripening. Further characterization of these populations is currently under process. Forty-eight percents (St-Marcellin) and 70% (Brie) of the samples were B. pseudolongum positive/E. coli negative while only 10% (St-Marcellin) and 3% (Brie) were B. pseudolongum negative/E. coli positive. CONCLUSIONS The increase of total bifidobacteria during ripening in Marcellin's process does not allow their use as fecal indicator. The presence of B. pseudolongum along the processes defined a contamination from animal origin since this species is predominant in cow dung and has never been isolated in human feces. B. pseudolongum was more sensitive as an indicator than E. coli along the two different cheese processes. B. pseudolongum should be used as fecal indicator rather than E. coli to assess the quality of raw milk and raw milk cheeses.
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Affiliation(s)
- Véronique Delcenserie
- Food Sciences Department, Faculty of Veterinary Medicine, University of Liège, Sart Tilman, B43b Liege, B-4000 Belgium
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Pokusaeva K, Fitzgerald GF, van Sinderen D. Carbohydrate metabolism in Bifidobacteria. GENES AND NUTRITION 2011; 6:285-306. [PMID: 21484167 DOI: 10.1007/s12263-010-0206-6] [Citation(s) in RCA: 499] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/15/2010] [Indexed: 12/17/2022]
Abstract
Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plant-derived oligo- and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.
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Affiliation(s)
- Karina Pokusaeva
- Alimentary Pharmabiotic Centre, Department of Microbiology, University College Cork, Western Road, Cork, Ireland
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Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Syst Appl Microbiol 2010; 33:359-66. [DOI: 10.1016/j.syapm.2010.08.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 08/30/2010] [Accepted: 08/31/2010] [Indexed: 11/17/2022]
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Endo A, Futagawa-Endo Y, Dicks LMT. Diversity of Lactobacillus and Bifidobacterium in feces of herbivores, omnivores and carnivores. Anaerobe 2010; 16:590-6. [PMID: 21034840 DOI: 10.1016/j.anaerobe.2010.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/08/2010] [Accepted: 10/20/2010] [Indexed: 12/21/2022]
Abstract
The Lactobacillus and Bifidobacterium population in the feces of 26 animals (16 species) were studied by culture-dependent and culture-independent techniques. Lactobacilli were detected from a few herbivores, all carnivores and some omnivores. Lactobacillus johnsonii, Lactobacillus reuteri, Lactobacillus salivarius, Lactobacillus vaginalis and Lactobacillus ingluviei were the most dominant lactobacilli in carnivores. These species were, however, not predominant in herbivores and omnivores. Lactobacillus brevis, Lactobacillus casei, Lactobacillus parabuchneri, Lactobacillus plantarum, Lactobacillus sakei, Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides, usually present in raw plant material, were present in omnivores but not in carnivores. Bifidobacteria were detected in only four herbivores and two omnivores. Bifidobacterium pseudolongum was the only Bifidobacterium species detected in herbivores. Bifidobacteria detected in the two omnivores are phylogenetically not closely related to known species and are possible novel species in the genus.
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Affiliation(s)
- Akihito Endo
- Department of Microbiology, University of Stellenbosch, South Africa.
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Killer J, Kopečný J, Mrázek J, Koppová I, Havlík J, Benada O, Kott T. Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. Int J Syst Evol Microbiol 2010; 61:1315-1321. [PMID: 20656822 DOI: 10.1099/ijs.0.022525-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA and heat-shock protein 60 (hsp60) gene sequences. Analysis of 16S rRNA gene sequence similarities revealed that the isolates of the first group were affiliated to Bifidobacterium asteroides YIT 11866(T), B. indicum JCM 1302(T) and B. coryneforme ATCC 25911(T) (96.2, 96.0 and 95.9 % sequence similarity, respectively), together with other bifidobacteria showing lower sequence similarity. Additional representatives of the second group were found to be affiliated to Bifidobacterium minimum YIT 4097(T) and B. coryneforme ATCC 25911(T) (96.0 and 96.3 % sequence similarity) and also to other bifidobacteria with lower sequence similarity. These results indicate that the isolates of the two groups belong to novel species within the genus Bifidobacterium. This observation was further substantiated by the results of partial sequencing of hsp60. On the basis of phylogenetic and phenotypic analyses and analysis of 16S rRNA and partial hsp60 gene sequences, we propose two novel species, Bifidobacterium actinocoloniiforme sp. nov. (type strain LISLUCIII-P2(T) = DSM 22766(T) = CCM 7728(T)) and Bifidobacterium bohemicum sp. nov. (type strain JEMLUCVIII-4(T) = DSM 22767(T) = CCM 7729(T)).
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Affiliation(s)
- J Killer
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 - Krč 142 20, Czech Republic
| | - J Kopečný
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 - Krč 142 20, Czech Republic
| | - J Mrázek
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 - Krč 142 20, Czech Republic
| | - I Koppová
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 - Krč 142 20, Czech Republic
| | - J Havlík
- Czech University of Life Sciences, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 - Suchdol 165 21, Czech Republic
| | - O Benada
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 - Krč 142 20, Czech Republic
| | - T Kott
- Institute of Animal Science, Přátelství 815, Prague - Uhříněves 104 00, Czech Republic
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