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Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
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Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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Colonized Niche, Evolution and Function Signatures of Bifidobacterium pseudolongum within Bifidobacterial Genus. Foods 2021; 10:foods10102284. [PMID: 34681333 PMCID: PMC8535030 DOI: 10.3390/foods10102284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Although genomic features of various bifidobacterial species have received much attention in the past decade, information on Bifidobacterium pseudolongum was limited. In this study, we retrieved 887 publicly available genomes of bifidobacterial species, and tried to elucidate phylogenetic and potential functional roles of B. pseudolongum within the Bifidobacterium genus. Results: The results indicated that B. pseudolongum formed a population structure with multiple monophyletic clades, and had established associations with different types of mammals. The abundance of B. pseudolongum was inversely correlated with that of the harmful gut bacterial taxa. We also found that B. pseudolongum showed a strictly host-adapted lifestyle with a relatively smaller genome size, and higher intra-species genetic diversity in comparison with the other tested bifidobacterial species. For functional aspects, B. pseudolongum showed paucity of specific metabolic functions, and enrichment of specific enzymes degrading complex plant carbohydrates and host glycans. In addition, B. pseudolongum possessed a unique signature of probiotic effector molecules compared with the other tested bifidobacterial species. The investigation on intra-species evolution of B. pseudolongum indicated a clear evolution trajectory in which considerable clade-specific genes, and variation on genomic diversity by clade were observed. Conclusions: These findings provide valuable information for explaining the host adaptability of B. pseudolongum, its evolutionary role, as well as its potential probiotic effects.
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Wang B, Luo H. Effects of mulberry leaf silage on antioxidant and immunomodulatory activity and rumen bacterial community of lambs. BMC Microbiol 2021; 21:250. [PMID: 34544373 PMCID: PMC8454139 DOI: 10.1186/s12866-021-02311-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
Background Rumen is a natural fermentation system and the microorganisms inside can effectively utilize plant bioresource and interact with host metabolism. Here, analysis of rumen microbiome, together with animal performance and serum metabolism in a lamb model were performed to identify the potential use of mulberry leaf silage (MS) to replace alfalfa silage (AS) as a new functional feed resource and to mining the novel specific mulberry leaf associated rumen bacteria interact with host metabolism. Results The lambs fed with MS diet showed improved antioxidant capacity and immune function compared to those fed AS diet. The MS diet significantly altered rumen microbiota α- and β-diversity and taxonomic composition. Microbial analysis revealed that Bifidobacterium, Lactobacillus and Schwartzia were enhanced, and Ruminococcaceae UCG-010 and Lachnospiraceae_XPB1014_group were down-regulated in the rumen of MS group. A strong association was also found between these rumen microbial taxa and host antioxidant and immunomodulatory capacity. Conclusion These findings indicated that mulberry leaf silage can be a high-quality feed source or bioactive pharmaceutical that is responsible for ruminant’s health benefits. The modified rumen microbial community by mulberry leaf silage were associated with the enhanced antioxidant capacity and immunomodulatory of lambs. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02311-1.
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Affiliation(s)
- Bing Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hailing Luo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Kumar A, Hussain SA, Prasad W, Singh AK, Singh R. Effect of oxygen tolerant probiotic strain, stabilizers and copper addition on the storage stability of Aloe vera supplemented synbiotic lassi. FUTURE FOODS 2021. [DOI: 10.1016/j.fufo.2021.100021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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5
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Luo Y, Xiao Y, Zhao J, Zhang H, Chen W, Zhai Q. The role of mucin and oligosaccharides via cross-feeding activities by Bifidobacterium: A review. Int J Biol Macromol 2020; 167:1329-1337. [PMID: 33202267 DOI: 10.1016/j.ijbiomac.2020.11.087] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are one genus of low-abundance gut commensals that are often associated with host health-promoting effects. Bifidobacteria can degrade various dietary fibers (i.e., galactooligosaccharides, fructooligosaccharides, inulin), and are reported as one of the few gut-dwelling microbes that can utilize host-derived carbohydrates (mucin and human milk oligosaccharides). Previous studies have noted that the superior carbohydrate-metabolizing abilities of bifidobacteria facilitate the intestinal colonization of this genus and also benefit other gut symbionts, in particular butyrate-producing bacteria, via cooperative metabolic interactions. Given that such cross-feeding activities of bifidobacteria on mucin and oligosaccharides have not been systematically summarized, here we review the carbohydrate-degrading capabilities of various bifidobacterial strains that were identified in vitro experiments, the core enzymes involved in the degradation mechanisms, and social behavior between bifidobacteria and other intestinal microbes, as well as among species-specific bifidobacterial strains. The purpose of this review is to enhance our understanding of the interactions of prebiotics and probiotics, which sheds new light on the future use of oligosaccharides and bifidobacteria for nutritional intervention or clinical application.
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Affiliation(s)
- Yanhong Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China; Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
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Campaniello D, Bevilacqua A, Speranza B, Sinigaglia M, Corbo MR. Alginate- and Gelatin-Coated Apple Pieces as Carriers for Bifidobacterium animalis subsp. lactis DSM 10140. Front Microbiol 2020; 11:566596. [PMID: 33178152 PMCID: PMC7597366 DOI: 10.3389/fmicb.2020.566596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023] Open
Abstract
Fruit and vegetables are considered good natural supports for microorganisms; however, probiotics could cause negative changes on some organoleptic and sensory traits. Thus, the main topic of this paper was the design of coated apple chips as carriers for probiotics with a high level of sensory traits. The research was divided into two steps. First, four functional strains (Limosilactobacillus reuteri DSM 20016, Bifidobacterium animalis subsp. lactis DSM 10140, and Lactiplantibacillus plantarum c16 and c19) were immobilized on apple pieces through dipping of fruit chips in probiotic suspensions for different contact times (from 15 to 30 min) and stored at 4°C for 12 days. Periodically, the viable count was assessed. As a result of this step, a contact time of 15 min was chosen because it assured an optimal deposition of microorganisms. In the second step, apple pieces inoculated with B. animalis subsp. lactis DSM 10140 were coated with alginate and gelatin and stored at 4 and 8°C for 10 days; pH, microbiological counts, color (browning index), and sensory scores were evaluated. Bifidobacterium animalis DSM 10140 exerted a negative effect on apple chips and cause a significant browning; however, the use of coating counteracted this phenomenon. In fact, coated chips showed higher sensory scores and lower browning index. In addition, gelatin showed better performances in terms of probiotic viability, because at 8°C, a significant viability loss of B. animalis DSM 10140 (1.2 log cfu/g) was found on alginate-coated chips. Gelatin-coated apple pieces with B. animalis subsp. lactis DSM 10140 could be an attractive functional food for a wide audience, although further investigations are required on in vivo effects of this product after consumption.
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Affiliation(s)
- Daniela Campaniello
- Department of the Science of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Barbara Speranza
- Department of the Science of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Milena Sinigaglia
- Department of the Science of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
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Strategic Measures for Food Processing and Manufacturing Facilities to Combat Coronavirus Pandemic (COVID-19). JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.2.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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8
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Turchi B, Mancini S, Pastorelli R, Viti C, Tronconi L, Bertelloni F, Felicioli A, Cerri D, Fratini F, Paci G. Dietary supplementation of chestnut and quebracho tannins mix: Effect on caecal microbial communities and live performance of growing rabbits. Res Vet Sci 2019; 124:129-136. [PMID: 30897395 DOI: 10.1016/j.rvsc.2019.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 01/16/2023]
Abstract
The interest in antimicrobial compounds as feed additives is currently increasing. Among different options, tannins seem to have several beneficial effects when employed in animals diet. The present study aimed at investigating the influence on caecal microbial communities of the supplementation of a chestnut and quebracho tannins mix in meat rabbit's diet, also considering animals live performances. Four groups of rabbits were fed with a different diet: a control diet (C); a control diet with coccidiostat (CC), and two experimental diets with 0.3% (T0.3) and 0.6% (T0.6) chestnut and quebracho tannins mix. For microbial analysis, culture-dependent and culture-independent methods were employed. Live performances were not significantly affected by tannins mix supplementations, as well as culturable microbial loads of E. coli, Enterobacteriaceae, Bacteroides spp. and Bifidobacterium spp. C. perfringens was always under the detection limit. A consistent result was obtained by qPCR. As for PCR-DGGE analysis, the Richness and evenness (Shannon-Weiner index) of bacterial communities in caecum resulted significantly higher in control samples (C and CC) than in those from rabbit fed with tannin-containing diets. Sequencing analysis revealed that the phylum Firmicutes was less represented in samples from control groups. As for the methanogen archaeal DGGE, no significant differences were found in richness and diversity among different groups, all dominated by Methanobrevibacter spp.. This work highlights the potential antimicrobial effect of chestnut and quebracho tannins mix in an in vivo system revealed by molecular analysis.
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Affiliation(s)
- Barbara Turchi
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
| | - Simone Mancini
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy
| | - Roberta Pastorelli
- Research Centre for Agriculture and Environment, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'economia Agraria (CREA-AA), via di Lanciola 12/A, Firenze, Italy.
| | - Carlo Viti
- Department of Agri-Food Production and Environmental Sciences, Section of Agricultural Microbiology, University of Florence, Piazzale delle Cascine 18, Firenze, Italy.
| | - Laura Tronconi
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy
| | - Fabrizio Bertelloni
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
| | - Antonio Felicioli
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
| | - Domenico Cerri
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
| | - Filippo Fratini
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
| | - Gisella Paci
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, Pisa, Italy.
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Fontana A, Zacconi C, Morelli L. Genetic Signatures of Dairy Lactobacillus casei Group. Front Microbiol 2018; 9:2611. [PMID: 30425707 PMCID: PMC6218691 DOI: 10.3389/fmicb.2018.02611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/12/2018] [Indexed: 11/25/2022] Open
Abstract
Lactobacillus casei/Lactobacillus paracasei group of species contains strains adapted to a wide range of environments, from dairy products to intestinal tract of animals and fermented vegetables. Understanding the gene acquisitions and losses that induced such different adaptations, implies a comparison between complete genomes, since evolutionary differences spread on the whole sequence. This study compared 12 complete genomes of L. casei/paracasei dairy-niche isolates and 7 genomes of L. casei/paracasei isolated from other habitats (i.e., corn silage, human intestine, sauerkraut, beef, congee). Phylogenetic tree construction and average nucleotide identity (ANI) metric showed a clustering of the two dairy L. casei strains ATCC393 and LC5, indicating a lower genetic relatedness in comparison to the other strains. Genomic analysis revealed a core of 313 genes shared by dairy and non-dairy Lactic Acid bacteria (LAB), within a pan-genome of 9,462 genes. Functional category analyses highlighted the evolutionary genes decay of dairy isolates, particularly considering carbohydrates and amino acids metabolisms. Specifically, dairy L. casei/paracasei strains lost the ability to metabolize myo-inositol and taurine (i.e., iol and tau gene clusters). However, gene acquisitions by dairy strains were also highlighted, mostly related to defense mechanisms and host-pathogen interactions (i.e., yueB, esaA, and sle1). This study aimed to be a preliminary investigation on dairy and non-dairy marker genes that could be further characterized for probiotics or food applications.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process-DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Carla Zacconi
- Department for Sustainable Food Process-DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process-DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Satti M, Tanizawa Y, Endo A, Arita M. Comparative analysis of probiotic bacteria based on a new definition of core genome. J Bioinform Comput Biol 2018; 16:1840012. [PMID: 29792377 DOI: 10.1142/s0219720018400127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories "amino acid transport and metabolism" representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.
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Affiliation(s)
- Maria Satti
- * Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- † Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Akihito Endo
- ‡ Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099-2493, Japan
| | - Masanori Arita
- † Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.,§ RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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11
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Zhang Y, Liu Q, Zhang W, Zhang Z, Wang W, Zhuang S. Gastrointestinal microbial diversity and short-chain fatty acid production in pigs fed different fibrous diets with or without cell wall-degrading enzyme supplementation. Livest Sci 2018. [DOI: 10.1016/j.livsci.2017.11.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Godoy AS, Camilo CM, Kadowaki MA, Muniz HDS, Espirito Santo M, Murakami MT, Nascimento AS, Polikarpov I. Crystal structure of β1→6-galactosidase fromBifidobacterium bifidumS17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose. FEBS J 2016; 283:4097-4112. [DOI: 10.1111/febs.13908] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/05/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022]
Affiliation(s)
| | | | | | | | | | - Mario Tyago Murakami
- Biosciences National Laboratory; National Center for Energy and Materials Research; Campinas Brazil
| | | | - Igor Polikarpov
- Departamento de Física em São Carlos; Universidade de São Paulo; Brazil
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Wang J, Fan H, Han Y, Zhao J, Zhou Z. Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:100-110. [PMID: 27383798 PMCID: PMC5205584 DOI: 10.5713/ajas.16.0166] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/22/2016] [Accepted: 06/28/2016] [Indexed: 11/27/2022]
Abstract
Objective The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep’s health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of sheep. Methods This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. Results The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum), small intestine (duodenum, jejunum, and ileum), and large intestine (cecum, colon, and rectum). Conclusion This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.
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Affiliation(s)
- Jin Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Fan
- Tianjin Institute of Animal Husbandry and Veterinary Research, Tianjin 300384, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Ye Han
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jinzhao Zhao
- Tianjin Kuntai Environment & Energy Science and Technology Development Co., Ltd, Tianjin 300191, China
| | - Zhijiang Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Kim M, Wells JE. A Meta-analysis of Bacterial Diversity in the Feces of Cattle. Curr Microbiol 2015; 72:145-151. [PMID: 26542532 DOI: 10.1007/s00284-015-0931-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/26/2015] [Indexed: 12/29/2022]
Abstract
In this study, we conducted a meta-analysis on 16S rRNA gene sequences of bovine fecal origin that are publicly available in the RDP database. A total of 13,663 sequences including 603 isolate sequences were identified in the RDP database (Release 11, Update 1), where 13,447 sequences were assigned to 10 phyla, 17 classes, 28 orders, 59 families, and 110 genera, while the remaining 216 sequences could not be assigned to a known phylum. Firmicutes and Bacteroidetes were the first and the second predominant phyla, respectively. About 41 % of the total sequences could not be assigned to a known genus. The total sequences were assigned to 1252 OTUs at 97 % sequence similarity. A small number of OTUs shared among datasets indicate that fecal bacterial communities of cattle are greatly affected by various factors, specifically diet. This study may guide future studies to further analyze fecal bacterial communities of cattle.
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Affiliation(s)
- Minseok Kim
- U.S. Department of Agriculture, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, NE, 68933, USA
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - James E Wells
- U.S. Department of Agriculture, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, NE, 68933, USA.
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15
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Pacchioni RG, Carvalho FM, Thompson CE, Faustino ALF, Nicolini F, Pereira TS, Silva RCB, Cantão ME, Gerber A, Vasconcelos ATR, Agnez-Lima LF. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. Microbiologyopen 2014; 3:299-315. [PMID: 24706600 PMCID: PMC4082704 DOI: 10.1002/mbo3.169] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/23/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas.
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Affiliation(s)
- Ralfo G Pacchioni
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, Brazil
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Fermentation of mucin by bifidobacteria from rectal samples of humans and rectal and intestinal samples of animals. Folia Microbiol (Praha) 2011; 56:85-9. [PMID: 21468760 DOI: 10.1007/s12223-011-0022-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 06/29/2010] [Indexed: 10/18/2022]
Abstract
Bifidobacteria (246 strains in total) were isolated from rectal samples of infants and adult humans and animals, and from intestinal samples of calves. Twenty-five strains grew well on mucin: 20 from infants, two from adults, and three from goatlings. Poor or no growth on mucin was observed in 156 bifidobacterial strains of animal origin. The difference between human and animal isolates in ability to grow on mucin was significant at p < 0.001. Nine human strains with the best growth on mucin were identified as Bifidobacterium bifidum. These strains produced extracellular, membrane-bound, and intracellular mucinases with activities of 0.11, 0.53, and 0.09 μmol/min of reducing sugars per milligram of protein, respectively. Membrane-bound mucinases were active between pH 5 and 10. The optimum pH of extracellular mucinases was 6-7. Fermentation patterns in cultures grown on mucin and glucose differed. On mucin, the acetate-to-lactate ratio was higher than in cultures grown on glucose (p = 0.012). We showed that the bifidobacteria belong to the mucin-fermenting bacteria in humans, but their significance in mucin degradation in animals seems to be limited.
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Cronin M, Ventura M, Fitzgerald GF, van Sinderen D. Progress in genomics, metabolism and biotechnology of bifidobacteria. Int J Food Microbiol 2011; 149:4-18. [PMID: 21320731 DOI: 10.1016/j.ijfoodmicro.2011.01.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/06/2011] [Accepted: 01/10/2011] [Indexed: 12/16/2022]
Abstract
Members of the genus Bifidobacterium were first described over a century ago and were quickly associated with a healthy intestinal tract due to their numerical dominance in breast-fed babies as compared to bottle-fed infants. Health benefits elicited by bifidobacteria to its host, as supported by clinical trials, have led to their wide application as probiotic components of health-promoting foods, especially in fermented dairy products. However, the relative paucity of genetic tools available for bifidobacteria has impeded development of a comprehensive molecular understanding of this genus. In this review we present a summary of current knowledge on bifidobacterial metabolism, classification, physiology and genetics and outline the currently available methods for genetically accessing and manipulating the genus.
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Affiliation(s)
- Michelle Cronin
- Cork Cancer Research Centre, Mercy University Hospital and Leslie C. Quick Jnr. Laboratory, University College Cork, Cork, Ireland
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Yeo SK, Liong MT. Effect of prebiotics on viability and growth characteristics of probiotics in soymilk. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2010; 90:267-275. [PMID: 20355041 DOI: 10.1002/jsfa.3808] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND Soy products have attracted much attention lately as carriers for probiotics. This study was aimed at enhancing the growth of probiotics in soymilk via supplementation with prebiotics. RESULTS Lactobacillus sp. FTDC 2113, Lactobacillus acidophilus FTDC 8033, Lactobacillus acidophilus ATCC 4356, Lactobacillus casei ATCC 393, Bifidobacterium FTDC 8943 and Bifidobacterium longum FTDC 8643 were evaluated for their viability and growth characteristics in prebiotic-supplemented soymilk. In the presence of fructooligosaccharides (FOS), inulin, mannitol, maltodextrin and pectin, all strains showed viability exceeding 7 log(10) colony-forming units mL(-1) after 24 h. Their growth was significantly (P < 0.05) increased on supplementation with maltodextrin, pectin, mannitol and FOS. Additionally, supplementation with FOS, mannitol and maltodextrin increased (P < 0.05) the production of lactic acid. Supplementation with FOS and maltodextrin also increased the alpha-galactosidase activity of probiotics, leading to enhanced hydrolysis and utilisation of soy oligosaccharides. Finally, prebiotic supplementation enhanced the utilisation of simpler sugars such as fructose and glucose in soymilk. CONCLUSION Supplementation with prebiotics enhances the potential of soymilk as a carrier for probiotics.
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Affiliation(s)
- Siok-Koon Yeo
- School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang, Malaysia
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Metzler B, Vahjen W, Baumgärtel T, Rodehutscord M, Mosenthin R. Changes in bacterial populations in the ileum of pigs fed low-phosphorus diets supplemented with different sources of fermentable carbohydrates. Anim Feed Sci Technol 2009. [DOI: 10.1016/j.anifeedsci.2008.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ventura M, Canchaya C, Fitzgerald GF, Gupta RS, van Sinderen D. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie van Leeuwenhoek 2006; 91:351-72. [PMID: 17072531 DOI: 10.1007/s10482-006-9122-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 09/28/2006] [Indexed: 10/24/2022]
Abstract
The field of microbiology has in recent years been transformed by the ever increasing number of publicly available whole-genome sequences. This sequence information has significantly enhanced our understanding of the physiology, genetics and evolutionary development of bacteria. Among the latter group of microorganisms, bifidobacteria represent important human commensals because of their perceived contribution to maintaining a balanced gastrointestinal tract microbiota. In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For this reason, these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. Recent genome sequencing of a number of bifidobacterial species has allowed access to the complete genetic make-up of these bacteria. In this review we will discuss how genomic data has allowed us to understand bifidobacterial evolution, while also revealing genetic functions that explains their presence in the particular ecological environment of the gastrointestinal tract.
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Affiliation(s)
- Marco Ventura
- Department of Genetics, Anthropology and Evolution, University of Parma, Parma, Italy.
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Amaretti A, Tamburini E, Bernardi T, Pompei A, Zanoni S, Vaccari G, Matteuzzi D, Rossi M. Substrate preference of Bifidobacterium adolescentis MB 239: compared growth on single and mixed carbohydrates. Appl Microbiol Biotechnol 2006; 73:654-62. [PMID: 16865345 DOI: 10.1007/s00253-006-0500-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 05/08/2006] [Accepted: 05/14/2006] [Indexed: 11/29/2022]
Abstract
The utilization of mono-, di-, and oligosaccharides by Bifidobacterium adolescentis MB 239 was investigated. Raffinose, fructooligosaccharides (FOS), lactose, and the monomeric moieties glucose and fructose were used. To establish a hierarchy of sugars preference, the kinetics of growth and sugar consumption were determined on individual and mixed carbohydrates. On single carbon sources, higher specific growth rates and cell yields were attained on di- and oligosaccharides compared to monosaccharides. Analysis of the carbohydrates in steady-state chemostat cultures, growing at the same dilution rate on FOS, lactose, or raffinose, showed that monomeric units and hydrolysis products were present. In chemostat cultures on individual carbohydrates, B. adolescentis MB 239 simultaneously displayed alpha-galactosidase, beta-galactosidase, and beta-fructofuranosidase activities on all the sugars, including monosaccharides. Glycosyl hydrolytic activities were found in cytosol, cell surface, and growth medium. Batch experiments on mixtures of carbohydrates showed that they were co-metabolized by B. adolescentis MB 239, even if different disappearance kinetics were registered. When mono-, di-, and oligosaccharides were simultaneously present in the medium, no precedence for monosaccharides utilization was observed, and di- and oligosaccharides were consumed before their constitutive moieties.
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Affiliation(s)
- Alberto Amaretti
- Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy
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Sirotek K, Slováková L, Kopecný J, Marounek M. Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rabbit caecal bacterium Bacteroides caccae. Lett Appl Microbiol 2004; 38:327-32. [PMID: 15214734 DOI: 10.1111/j.1472-765x.2004.01492.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To compare fermentation pattern in cultures of Bacteroides caccae supplied with pectin and glucose, and identify enzymes involved in metabolism of pectin. METHODS AND RESULTS A strain KWN isolated from the rabbit caecum was used. Fermentation pattern, changes of viscosity and enzyme reactions products were determined. Cultures grown on pectin produced significantly more acetate and less formate, lactate, fumarate and succinate than cultures grown on glucose. Production of cell dry matter and protein per gram of substrate used was the same in pectin- and glucose-grown cultures. The principal enzymes that participated in the metabolism of pectin were extracellular exopectate hydrolase (EC 3.2.1.67), extracellular endopectate lyase (EC 4.2.2.2) and cell-associated 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (EC 4.1.2.14). The latter enzyme is unique to the Entner-Doudoroff pathway. Activities of pectinolytic enzymes in cultures grown on glucose were low. Activity of KDPG aldolase was similar in pectin- and glucose-grown cells. CONCLUSIONS Metabolites and activities of pectin-degrading enzymes differed in cultures of B. caccae KWN grown on pectin and glucose. Yields of dry matter and protein were the same on both substrates. SIGNIFICANCE AND IMPACT OF THE STUDY Information on metabolism of pectin in animal strains of Bacteroides is incomplete. This study extends the knowledge on metabolism in bacteria from the rabbit caecum.
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Affiliation(s)
- K Sirotek
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czech Republic
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Simpson PJ, Stanton C, Fitzgerald GF, Ross RP. Genomic diversity and relatedness of bifidobacteria isolated from a porcine cecum. J Bacteriol 2003; 185:2571-81. [PMID: 12670982 PMCID: PMC152629 DOI: 10.1128/jb.185.8.2571-2581.2003] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study initially involved the isolation of a number of bifidobacteria from either the lumen or the epithelium of a porcine cecum. A total of 160 isolates were selected at random on MRS plates containing cysteine hydrochloride (0.5 g/liter) and mupirocin (50 mg/liter). All were identified as bifidobacteria based on fructose-6-phosphate phosphoketolase activity. Following genomic digestion with the restriction enzyme XbaI and pulsed-field gel electrophoresis (PFGE), the isolates produced 15 distinct macro-restriction patterns. Several of the PFGE patterns differed by only 1, 2, or 3 DNA fragments and were grouped as related patterns into seven PFGE types, termed A through G. The related patterns appeared to show genomic plasticity within the isolates arising from chromosomal mutations or possibly horizontal transfer of plasmids. The relative frequency of each PFGE type was maintained within each cecal sample, with PFGE type E representing approximately 50% of the isolates. Randomly amplified polymorphic DNA PCR, cell morphology, whole-cell protein profiling, 16S ribosomal DNA sequencing, and DNA-DNA hybridization were used to determine if the seven apparently unrelated PFGE types represented genetically distinct isolates. Four groups were identified: PFGE types A, C/D/G, B/E, and F, and these appeared to represent Bifidobacterium minimum, Bifidobacterium pseudolongum subsp. pseudolongum, and Bifidobacterium pseudolongum subsp. globosum and two new species, respectively. The data demonstrate the presence of considerable genomic diversity within a relatively simple bifidobacteria population, consisting of 15 distinct strains representing four groups, which was maintained throughout the porcine cecal contents and epithelial layer.
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Affiliation(s)
- P J Simpson
- Teagasc, Dairy Products Research Centre, Moorepark, Fermoy, County Cork, Ireland
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