1
|
Li S, You X, Rani A, Özcan E, Sela DA. Bifidobacterium infantis utilizes N-acetylglucosamine-containing human milk oligosaccharides as a nitrogen source. Gut Microbes 2023; 15:2244721. [PMID: 37609905 PMCID: PMC10448974 DOI: 10.1080/19490976.2023.2244721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
Bifidobacterium longum subsp. infantis (B. infantis) utilizes oligosaccharides secreted in human milk as a carbohydrate source. These human milk oligosaccharides (HMOs) integrate the nitrogenous residue N-acetylglucosamine (NAG), although HMO nitrogen utilization has not been described to date. Herein, we characterize the B. infantis nitrogen utilization phenotype on two NAG-containing HMO species, LNT and LNnT. This was characterized through in vitro growth kinetics, incorporation of isotopically labeled NAG nitrogen into the proteome, as well as modulation of intracellular 2-oxoglutarate levels while utilizing HMO nitrogen. Further support is provided by comparative transcriptomics and proteomics that identified global regulatory networks deployed during HMO nitrogen utilization. The aggregate data demonstrate that B. infantis strains utilize HMO nitrogen with the potential to significantly impact fundamental and clinical studies, as well as enable applications.
Collapse
Affiliation(s)
- Shuqi Li
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Xiaomeng You
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Ezgi Özcan
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA, USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
2
|
Ramoneda J, Jensen TBN, Price MN, Casamayor EO, Fierer N. Taxonomic and environmental distribution of bacterial amino acid auxotrophies. Nat Commun 2023; 14:7608. [PMID: 37993466 PMCID: PMC10665431 DOI: 10.1038/s41467-023-43435-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of 'streamlined' life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.
Collapse
Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, USA.
| | - Thomas B N Jensen
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, USA
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emilio O Casamayor
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), Blanes, Spain
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| |
Collapse
|
3
|
Kiernan DP, O’Doherty JV, Sweeney T. The Effect of Prebiotic Supplements on the Gastrointestinal Microbiota and Associated Health Parameters in Pigs. Animals (Basel) 2023; 13:3012. [PMID: 37835619 PMCID: PMC10572080 DOI: 10.3390/ani13193012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Establishing a balanced and diverse microbiota in the GIT of pigs is crucial for optimizing health and performance throughout the production cycle. The post-weaning period is a critical phase, as it is often associated with dysbiosis, intestinal dysfunction and poor performance. Traditionally, intestinal dysfunctions associated with weaning have been alleviated using antibiotics and/or antimicrobials. However, increasing concerns regarding the prevalence of antimicrobial-resistant bacteria has prompted an industry-wide drive towards identifying natural sustainable dietary alternatives. Modulating the microbiota through dietary intervention can improve animal health by increasing the production of health-promoting metabolites associated with the improved microbiota, while limiting the establishment and proliferation of pathogenic bacteria. Prebiotics are a class of bioactive compounds that resist digestion by gastrointestinal enzymes, but which can still be utilized by beneficial microbes within the GIT. Prebiotics are a substrate for these beneficial microbes and therefore enhance their proliferation and abundance, leading to the increased production of health-promoting metabolites and suppression of pathogenic proliferation in the GIT. There are a vast range of prebiotics, including carbohydrates such as non-digestible oligosaccharides, beta-glucans, resistant starch, and inulin. Furthermore, the definition of a prebiotic has recently expanded to include novel prebiotics such as peptides and amino acids. A novel class of -biotics, referred to as "stimbiotics", was recently suggested. This bioactive group has microbiota-modulating capabilities and promotes increases in short-chain fatty acid (SCFA) production in a disproportionally greater manner than if they were merely substrates for bacterial fermentation. The aim of this review is to characterize the different prebiotics, detail the current understating of stimbiotics, and outline how supplementation to pigs at different stages of development and production can potentially modulate the GIT microbiota and subsequently improve the health and performance of animals.
Collapse
Affiliation(s)
- Dillon P. Kiernan
- School of Veterinary Medicine, University College Dublin, Belfield, D04 W6F6 Dublin, Ireland;
| | - John V. O’Doherty
- School of Agriculture and Food Science, University College Dublin, Belfield, D04 W6F6 Dublin, Ireland;
| | - Torres Sweeney
- School of Veterinary Medicine, University College Dublin, Belfield, D04 W6F6 Dublin, Ireland;
| |
Collapse
|
4
|
Kiernan DP, O’Doherty JV, Sweeney T. The Effect of Maternal Probiotic or Synbiotic Supplementation on Sow and Offspring Gastrointestinal Microbiota, Health, and Performance. Animals (Basel) 2023; 13:2996. [PMID: 37835602 PMCID: PMC10571980 DOI: 10.3390/ani13192996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The increasing prevalence of antimicrobial-resistant pathogens has prompted the reduction in antibiotic and antimicrobial use in commercial pig production. This has led to increased research efforts to identify alternative dietary interventions to support the health and development of the pig. The crucial role of the GIT microbiota in animal health and performance is becoming increasingly evident. Hence, promoting an improved GIT microbiota, particularly the pioneer microbiota in the young pig, is a fundamental focus. Recent research has indicated that the sow's GIT microbiota is a significant contributor to the development of the offspring's microbiota. Thus, dietary manipulation of the sow's microbiota with probiotics or synbiotics, before farrowing and during lactation, is a compelling area of exploration. This review aims to identify the potential health benefits of maternal probiotic or synbiotic supplementation to both the sow and her offspring and to explore their possible modes of action. Finally, the results of maternal sow probiotic and synbiotic supplementation studies are collated and summarized. Maternal probiotic or synbiotic supplementation offers an effective strategy to modulate the sow's microbiota and thereby enhance the formation of a health-promoting pioneer microbiota in the offspring. In addition, this strategy can potentially reduce oxidative stress and inflammation in the sow and her offspring, enhance the immune potential of the milk, the immune system development in the offspring, and the sow's feed intake during lactation. Although many studies have used probiotics in the maternal sow diet, the most effective probiotic or probiotic blends remain unclear. To this extent, further direct comparative investigations using different probiotics are warranted to advance the current understanding in this area. Moreover, the number of investigations supplementing synbiotics in the maternal sow diet is limited and is an area where further exploration is warranted.
Collapse
Affiliation(s)
- Dillon P. Kiernan
- School of Veterinary Medicine, University College Dublin, D04 C1P1 Dublin, Ireland;
| | - John V. O’Doherty
- School of Agriculture and Food Science, University College Dublin, D04 C1P1 Dublin, Ireland;
| | - Torres Sweeney
- School of Veterinary Medicine, University College Dublin, D04 C1P1 Dublin, Ireland;
| |
Collapse
|
5
|
Wu Y, Cao X, Du H, Guo X, Han Y, McClements DJ, Decker E, Xing B, Xiao H. Adverse effects of titanium dioxide nanoparticles on beneficial gut bacteria and host health based on untargeted metabolomics analysis. ENVIRONMENTAL RESEARCH 2023; 228:115921. [PMID: 37068726 DOI: 10.1016/j.envres.2023.115921] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/16/2023]
Abstract
Titanium dioxide (TiO2) is a common additive in foods, medicines, and personal care products. In recent years, nano-scale particles in TiO2 additives have been an increasing concern due to their potential adverse effects on human health, especially gut health. The objective of this study was to determine the impact of titanium dioxide nanoparticles (TiO2 NPs, 30 nm) on beneficial gut bacteria and host response from a metabolomics perspective. In the in vitro study, four bacterial strains, including Lactobacillus reuteri, Lactobacillus gasseri, Bifidobacterium animalis, and Bifidobacterium longum were subjected to the treatment of TiO2 NPs. The growth kinetics, cell viability, cell membrane permeability, and metabolomics response were determined. TiO2 NPs at the concentration of 200 μg/mL showed inhibitory effects on the growth of all four strains. The confocal microscope results indicated that the growth inhibitory effects could be associated with cell membrane damage caused by TiO2 NPs to the bacterial strains. Metabolomics analysis showed that TiO2 NPs caused alterations in multiple metabolic pathways of gut bacteria, such as tryptophan and arginine metabolism, which were demonstrated to play crucial roles in regulating gut and host health. In the in vivo study, mice were fed with TiO2 NPs (0.1 wt% in diet) for 8 weeks. Mouse urine was collected for metabolomics analysis and the tryptophan metabolism pathway was also significantly affected in TiO2 NPs-fed mice. Moreover, four neuroprotective metabolites were significantly reduced in both in vitro bacteria and in vivo urine samples. Overall, this study provides insights into the potential adverse effects of TiO2 NPs on gut bacteria and the metabolic responses of both bacteria and host. Further research is needed to understand the causality between gut bacteria composition and the metabolism pathway, which is critical to monitor the gut-microbiome mediated metabolome changes in toxicological assessment of food components.
Collapse
Affiliation(s)
- Yanyan Wu
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States
| | - Xiaoqiong Cao
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States
| | - Hengjun Du
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States
| | - Xiaojing Guo
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States
| | - Yanhui Han
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States
| | | | - Eric Decker
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, United States.
| |
Collapse
|
6
|
Dervisi I, Valassakis C, Koletti A, Kouvelis VN, Flemetakis E, Ouzounis CA, Roussis A. Evolutionary Aspects of Selenium Binding Protein (SBP). J Mol Evol 2023:10.1007/s00239-023-10105-4. [PMID: 37039856 DOI: 10.1007/s00239-023-10105-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
Selenium-binding proteins represent a ubiquitous protein family and recently SBP1 was described as a new stress response regulator in plants. SBP1 has been characterized as a methanethiol oxidase, however its exact role remains unclear. Moreover, in mammals, it is involved in the regulation of anti-carcinogenic growth and progression as well as reduction/oxidation modulation and detoxification. In this work, we delineate the functional potential of certain motifs of SBP in the context of evolutionary relationships. The phylogenetic profiling approach revealed the absence of SBP in the fungi phylum as well as in most non eukaryotic organisms. The phylogenetic tree also indicates the differentiation and evolution of characteristic SBP motifs. Main evolutionary events concern the CSSC motif for which Acidobacteria, Fungi and Archaea carry modifications. Moreover, the CC motif is harbored by some bacteria and remains conserved in Plants, while modified to CxxC in Animals. Thus, the characteristic sequence motifs of SBPs mainly appeared in Archaea and Bacteria and retained in Animals and Plants. Our results demonstrate the emergence of SBP from bacteria and most likely as a methanethiol oxidase.
Collapse
Affiliation(s)
- Irene Dervisi
- Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece
| | - Chrysanthi Valassakis
- Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece
| | - Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Vassilis N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece
| | - Emmanouil Flemetakis
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory, Centre for Research & Technology Hellas, Chemical Process & Energy Resources Institute, 54124, Thessaloníki, Greece
- Biological Computation & Computational Biology Group, AIIA Lab, School of Informatics, Aristotle University of Thessalonica, 57001, Thessaloníki, Greece
| | - Andreas Roussis
- Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece.
| |
Collapse
|
7
|
You X, Rani A, Özcan E, Lyu Y, Sela DA. Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome. Gut Microbes 2023; 15:2192546. [PMID: 36967532 PMCID: PMC10054289 DOI: 10.1080/19490976.2023.2192546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Human milk guides the structure and function of microbial commensal communities that colonize the nursing infant gut. Indigestible molecules dissolved in human milk establish a microbiome often dominated by bifidobacteria capable of utilizing these substrates. Interestingly, urea accounts for ~15% of total human milk nitrogen, representing a potential reservoir for microbiota that may be salvaged for critical metabolic operations during lactation and neonatal development. Accordingly, B. infantis strains are competent for urea nitrogen utilization, constituting a previously hypothetical phenotype in commensal bacteria hosted by humans. Urease gene expression, downstream nitrogen metabolic pathways, and enzymatic activity are induced during urea utilization to yield elevated ammonia concentrations. Moreover, biosynthetic networks relevant to infant nutrition and development are transcriptionally responsive to urea utilization including branched chain and other essential amino acids. Importantly, isotopically labeled urea nitrogen is broadly distributed throughout the expressed B. infantis proteome. This incisively demonstrates that the previously inaccessible urea nitrogen is incorporated into microbial products available for infant host utilization. In aggregate, B. infantis possesses the requisite phenotypic foundation to participate in human milk urea nitrogen recycling within its infant host and thus may be a key contributor to nitrogen homeostasis early in life.
Collapse
Affiliation(s)
- Xiaomeng You
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Ezgi Özcan
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Yang Lyu
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - David A Sela
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
- Department of Nutrition, University of Massachusetts, Amherst, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| |
Collapse
|
8
|
Cui S, Gu Z, Wang W, Tang X, Zhang Q, Mao B, Zhang H, Zhao J. Characterization of peptides available to different bifidobacteria. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Sadiq FA, Wenwei L, Wei C, Jianxin Z, Zhang H. Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms. MICROBIAL ECOLOGY 2022; 84:922-934. [PMID: 34676439 DOI: 10.1007/s00248-021-01904-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.
Collapse
Affiliation(s)
- Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Lu Wenwei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Chen Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Zhao Jianxin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
10
|
Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MC. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe 2022; 30:696-711.e5. [PMID: 35550672 DOI: 10.1016/j.chom.2022.04.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.
Collapse
Affiliation(s)
- Jumana Samara
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Health Sciences Centre, Winnipeg, MB, Canada
| | - Shirin Moossavi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, Canada
| | - Belal Alshaikh
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Van A Ortega
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Veronika Kuchařová Pettersen
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tahsin Ferdous
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Suzie L Hoops
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Amuchou Soraisham
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Joseph Vayalumkal
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deonne Dersch-Mills
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sagori Mukhopadhyay
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karen Puopolo
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Dan Knights
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jens Walter
- School of Microbiology, Department of Medicine, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harish Amin
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
11
|
Kwoji ID, Okpeku M, Adeleke MA, Aiyegoro OA. Formulation of Chemically Defined Media and Growth Evaluation of Ligilactobacillus salivarius ZJ614 and Limosilactobacillus reuteri ZJ625. Front Microbiol 2022; 13:865493. [PMID: 35602032 PMCID: PMC9121020 DOI: 10.3389/fmicb.2022.865493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/04/2022] [Indexed: 01/12/2023] Open
Abstract
Lactic acid bacteria are increasingly becoming important dietary supplements due to their health benefits when consumed in adequate quantity. The increasing attention on these important microbes has necessitated an in-depth understanding of their physiological processes, such as nutritional requirements and growth patterns, to better harness their probiotic potentials. This study was carried out to determine the nutritional requirements for the growth of L. salivarius ZJ614 and L. reuteri ZJ625 from a chemically defined medium and evaluate growth kinetics by fitting different sigmoidal growth models. The complete CDM contains 49 nutritional ingredients such as glucose, Tween 80®, mineral salts, buffers, amino acids, vitamins, and nucleotides at defined concentrations. In addition, the minimal nutritional requirements of the isolates were determined in a series of single-omission experiments (SOEs) to compose the MDM. Growth curve data were generated by culturing in an automated 96-well micro-plate reader at 37°C for 36 h, and photometric readings (optical density: OD600) were taken. The data were summarized in tables and charts using Microsoft Excel, while growth evaluation was carried out using open-source software (Curveball) on Python. The results revealed that omission of the amino acids, vitamins, and nucleotides groups resulted in 2.0, 20.17, and 60.24% (for L. salivarius ZJ614) and 0.95, 42.7, and 70.5% (for L. reuteri ZJ625) relative growths, respectively. Elimination of the individual CDM components also indicates varying levels of growth by the strains. The growth curve data revealed LogisticLag2 and Baranyi–Roberts models as the best fits for L. reuteri ZJ625 and L. salivarius ZJ614, respectively. All the strains showed appreciable growth on the CDM and MDM as observed in de Man–Rogosa–Sharpe (MRS) broth. We also described the growth kinetics of L. reuteri ZJ625 and L. salivarius ZJ614 in the CDM, and the best models revealed the estimated growth parameters.
Collapse
Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal Westville Campus, Durban, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal Westville Campus, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal Westville Campus, Durban, South Africa
- *Correspondence: Matthew Adekunle Adeleke
| | - Olayinka Ayobami Aiyegoro
- Gastrointestinal Microbiology and Biotechnology Unit, Agricultural Research Council-Animal Production Institute Irene, Pretoria, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| |
Collapse
|
12
|
Sew SW, Lu Y, Taniasuri F, Liu SQ. Chemical analysis and flavour compound changes of vegetable blend slurry fermented with selected probiotic bacteria. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
13
|
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome. Microorganisms 2022; 10:microorganisms10040740. [PMID: 35456791 PMCID: PMC9026213 DOI: 10.3390/microorganisms10040740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some amino acids (auxotrophs), while other members possess complete biosynthetic pathways for these nutrients (prototrophs). Metabolite exchange between auxotrophs and prototrophs affects microbial community structure. Previous studies of amino acid biosynthetic phenotypes were limited to model species or narrow taxonomic groups of bacteria. We analyzed over 2800 genomes representing 823 cultured HGM species with the aim to reconstruct biosynthetic pathways for proteinogenic amino acids. The genome context analysis of incomplete pathway variants allowed us to identify new potential enzyme variants in amino acid biosynthetic pathways. We further classified the studied organisms with respect to their pathway variants and inferred their prototrophic vs. auxotrophic phenotypes. A cross-species comparison was applied to assess the extent of conservation of the assigned phenotypes at distinct taxonomic levels. The obtained reference collection of binary metabolic phenotypes was used for predictive metabolic profiling of HGM samples from several large metagenomic datasets. The established approach for metabolic phenotype profiling will be useful for prediction of overall metabolic properties, interactions, and responses of HGM microbiomes as a function of dietary variations, dysbiosis and other perturbations.
Collapse
|
14
|
Schöpping M, Gaspar P, Neves AR, Franzén CJ, Zeidan AA. Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling. NPJ Syst Biol Appl 2021; 7:47. [PMID: 34887435 PMCID: PMC8660834 DOI: 10.1038/s41540-021-00207-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.
Collapse
Affiliation(s)
- Marie Schöpping
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Paula Gaspar
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark
| | - Ana Rute Neves
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark
- Arla Foods Ingredients Group P/S, 6920, Videbæk, Denmark
| | - Carl Johan Franzén
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Ahmad A Zeidan
- Systems Biology, Discovery, Chr. Hansen A/S, 2970, Hørsholm, Denmark.
| |
Collapse
|
15
|
Baker LM, Davies TS, Masetti G, Hughes TR, Marchesi JR, Jack AA, Joyce TSC, Allen MD, Plummer SF, Michael DR, Ramanathan G, Del Sol R, Facey PD. A genome guided evaluation of the Lab4 probiotic consortium. Genomics 2021; 113:4028-4038. [PMID: 34391865 DOI: 10.1016/j.ygeno.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/16/2021] [Accepted: 08/10/2021] [Indexed: 12/01/2022]
Abstract
In this study, we present the draft genome sequences of the Lab4 probiotic consortium using whole genome sequencing. Draft genome sequences were retrieved and deposited for each of the organisms; PRJNA559984 for B. bifidum CUL20, PRJNA482335 for Lactobacillus acidophilus CUL60, PRJNA482434 for Lactobacillus acid. Probiogenomic in silico analyses confirmed existing taxonomies and identified the presence putative gene sequences that were functionally related to the performance of each organism during in vitro assessments of bile and acid tolerability, adherence to enterocytes and susceptibility to antibiotics. Predictions of genomic stability identified no significant risk of horizontal gene transfer in any of the Lab4 strains and the absence of both antibiotic resistance and virulence genes. These observations were supported by the outcomes of acute phase and repeat dose tolerability studies in Wistar rats where challenge with high doses of Lab4 did not result in any mortalities, clinical/histopathological abnormalities nor indications of systemic toxicity. Detection of increased numbers of lactobacilli and bifidobacteria in the faeces of supplemented rats implied an ability to survive transit through the gastrointestinal tract and/or impact upon the intestinal microbiota composition. In summary, this study provides in silico, in vitro and in vivo support for probiotic functionality and the safety of the Lab4 consortium.
Collapse
Affiliation(s)
- L M Baker
- Swansea University Medical School, Swansea University, Singleton Park Campus, Swansea SA2 8PP, United Kingdom
| | - T S Davies
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - G Masetti
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - T R Hughes
- Systems Immunity Research Institute, Henry Welcome Building, Cardiff University, CF14 4XN, United Kingdom
| | - J R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - A A Jack
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - T S C Joyce
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - M D Allen
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - S F Plummer
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - D R Michael
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, United Kingdom
| | - G Ramanathan
- Pharmacology based Clinical Trials, Pennington Biomedical Research Center, 6400 Perkins Rd, Baton Rouge, LA 70808, USA
| | - R Del Sol
- Swansea University Medical School, Swansea University, Singleton Park Campus, Swansea SA2 8PP, United Kingdom
| | - P D Facey
- Swansea University Medical School, Swansea University, Singleton Park Campus, Swansea SA2 8PP, United Kingdom.
| |
Collapse
|
16
|
Engevik MA, Danhof HA, Hall A, Engevik KA, Horvath TD, Haidacher SJ, Hoch KM, Endres BT, Bajaj M, Garey KW, Britton RA, Spinler JK, Haag AM, Versalovic J. The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal. BMC Microbiol 2021; 21:154. [PMID: 34030655 PMCID: PMC8145834 DOI: 10.1186/s12866-021-02166-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium. RESULTS B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment. CONCLUSIONS Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract.
Collapse
Affiliation(s)
- Melinda A Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
- Department of Regernative Medicine & Cell Biology, Medical University of South Carolina, SC, Charleston, USA.
| | - Heather A Danhof
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anne Hall
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Kristen A Engevik
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Sigmund J Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Kathleen M Hoch
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Meghna Bajaj
- Department of Chemistry and Physics, and Department of Biotechnology, Alcorn State University, Lorman, MS, 39096, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Robert A Britton
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer K Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Anthony M Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| |
Collapse
|
17
|
Becken B, Davey L, Middleton DR, Mueller KD, Sharma A, Holmes ZC, Dallow E, Remick B, Barton GM, David LA, McCann JR, Armstrong SC, Malkus P, Valdivia RH. Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila. mBio 2021; 12:e00478-21. [PMID: 34006653 PMCID: PMC8262928 DOI: 10.1128/mbio.00478-21] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
The mucophilic anaerobic bacterium Akkermansia muciniphila is a prominent member of the gastrointestinal (GI) microbiota and the only known species of the Verrucomicrobia phylum in the mammalian gut. A high prevalence of A. muciniphila in adult humans is associated with leanness and a lower risk for the development of obesity and diabetes. Four distinct A. muciniphila phylogenetic groups have been described, but little is known about their relative abundance in humans or how they impact human metabolic health. In this study, we isolated and characterized 71 new A. muciniphila strains from a cohort of children and adolescents undergoing treatment for obesity. Based on genomic and phenotypic analysis of these strains, we found several phylogroup-specific phenotypes that may impact the colonization of the GI tract or modulate host functions, such as oxygen tolerance, adherence to epithelial cells, iron and sulfur metabolism, and bacterial aggregation. In antibiotic-treated mice, phylogroups AmIV and AmII outcompeted AmI strains. In children and adolescents, AmI strains were most prominent, but we observed high variance in A. muciniphila abundance and single phylogroup dominance, with phylogroup switching occurring in a small subset of patients. Overall, these results highlight that the ecological principles determining which A. muciniphila phylogroup predominates in humans are complex and that A. muciniphila strain genetic and phenotypic diversity may represent an important variable that should be taken into account when making inferences as to this microbe's impact on its host's health.IMPORTANCE The abundance of Akkermansia muciniphila in the gastrointestinal (GI) tract is linked to multiple positive health outcomes. There are four known A. muciniphila phylogroups, yet the prevalence of these phylogroups and how they vary in their ability to influence human health is largely unknown. In this study, we performed a genomic and phenotypic analysis of 71 A. muciniphila strains and identified phylogroup-specific traits such as oxygen tolerance, adherence, and sulfur acquisition that likely influence colonization of the GI tract and differentially impact metabolic and immunological health. In humans, we observed that single Akkermansia phylogroups predominate at a given time but that the phylotype can switch in an individual. This collection of strains provides the foundation for the functional characterization of A. muciniphila phylogroup-specific effects on the multitude of host outcomes associated with Akkermansia colonization, including protection from obesity, diabetes, colitis, and neurological diseases, as well as enhanced responses to cancer immunotherapies.
Collapse
Affiliation(s)
- Bradford Becken
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Duke University Hospital, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Dustin R Middleton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Katherine D Mueller
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Agastya Sharma
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Eric Dallow
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Brenna Remick
- Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Gregory M Barton
- Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Jessica R McCann
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Sarah C Armstrong
- Department of Pediatrics, Duke University Hospital, Durham, North Carolina, USA
| | - Per Malkus
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
18
|
Zhang X, Yang Y, Su J, Zheng X, Wang C, Chen S, Liu J, Lv Y, Fan S, Zhao A, Chen T, Jia W, Wang X. Age-related compositional changes and correlations of gut microbiome, serum metabolome, and immune factor in rats. GeroScience 2021; 43:709-725. [PMID: 32418021 PMCID: PMC8110635 DOI: 10.1007/s11357-020-00188-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Aging is a complex physiological process associated with degenerative disorder of metabolism and immune function, which contributes to the occurrence of senile diseases. The gut microbiota affects systemic inflammation in aging processes probably through metabolism, but their relationship is still unclear. In this study, 16S-rRNA-sequencing technology, gas chromatography-time-of-flight mass spectrometry (GC-TOFMS)-based metabolic profiling, and immune factor analysis combined with advanced differential and association analysis were employed to investigate the correlation between the microbiome, metabolome, and immune factors in male Wistar rats across lifespan. Our findings showed significant changes in the ileum microbiome and serum metabolome compositions across aging process. A two-level strategy was applied to demonstrate that key metabolites associated with age such as 4-hydroxyproline, proline, and lysine were clustered together and positively correlated with beneficial microbes including Bifidobacterium, Lactobacillus, and Akkermansia. Function analysis explored association between serum metabolite class and specific gut bacteria's metabolism pathways. Further correlation analysis on all the alteration patterns provided an interaction network of main immune factors such as IL-10, IgA, IgM, and IgG with key gut bacteria and serum metabolites. This study offers new insights into the relationship between immune factors, serum metabolome, and the gut microbiome.
Collapse
Affiliation(s)
- Xia Zhang
- Key Laboratory of Systems Biomedicine(Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuping Yang
- Key Laboratory of Systems Biomedicine(Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Juan Su
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, 210095, China
| | - Xiaojiao Zheng
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Chongchong Wang
- Key Laboratory of Systems Biomedicine(Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shaoqiu Chen
- Key Laboratory of Systems Biomedicine(Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiajian Liu
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Yingfang Lv
- Key Laboratory of Systems Biomedicine(Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shihao Fan
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, 210095, China
| | - Aihua Zhao
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Tianlu Chen
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Xiaoyan Wang
- Key Laboratory of Systems Biomedicine(Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
19
|
Wada M, Fukiya S, Suzuki A, Matsumoto N, Matsuo M, Yokota A. Methionine utilization by bifidobacteria: possible existence of a reverse transsulfuration pathway. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2021; 40:80-83. [PMID: 33520573 PMCID: PMC7817509 DOI: 10.12938/bmfh.2020-031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/07/2020] [Indexed: 01/04/2023]
Abstract
Although bifidobacteria are already widely used as beneficial microbes with
health-promoting effects, their amino acid utilization and metabolism are not yet fully
understood. Knowledge about the metabolism of sulfur-containing amino acids in
bifidobacteria is especially limited. In this study, we tested the methionine utilization
ability of several bifidobacterial strains when it was the sole available sulfur source.
Although bifidobacteria have long been predominantly considered to be cysteine auxotrophs,
we showed that this is not necessarily the case.
Collapse
Affiliation(s)
- Masaru Wada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.,Present address: Faculty of Agriculture, Setsunan University, 45-1 Nagaotouge-cho, Hirakata-shi, Osaka 573-0101, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Azusa Suzuki
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Nanae Matsumoto
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Miki Matsuo
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| |
Collapse
|
20
|
Abstract
Since their discovery, bifidobacteria have been considered to represent cornerstone commensal microorganisms in the host-microbiome interface at the intestinal level. Bifidobacteria have therefore enjoyed increasing scientific and commercial interest as a source of microorganisms with probiotic potential. However, since functional and probiotic traits are strictly strain-dependent, there is a constant need to isolate, cultivate, and characterize novel strains, activities that require the utilization of appropriate media, as well as robust isolation, cultivation, and preservation techniques. Besides, effective isolation of bifidobacteria from natural environments might require different manipulation and cultivation media and conditions depending on the specific characteristics of the sample material, the presence of competitive microbiota, the metabolic state in which bifidobacteria might be encountered within the sample and the particular metabolic traits of the bifidobacterial species adapted to such inhabitation.A wide array of culture media recipes have been described in the literature to routinely isolate and grow bifidobacteria under laboratory conditions. However, there is not a single and universally applicable medium for effective isolation, recovery, and cultivation of bifidobacteria, as each growth medium has its own particular advantages and limitations. Besides, the vast majority of these media formulations was not specifically formulated for these microorganisms, and thus information on bifidobacterial cultivation options is scarce while being scattered throughout literature. This chapter intends to serve as a resource summarizing the options to cultivate bifidobacteria that have been described to date, highlighting the main advantages and limitations of each of them.
Collapse
|
21
|
Lapierre FM, Schmid J, Ederer B, Ihling N, Büchs J, Huber R. Revealing nutritional requirements of MICP-relevant Sporosarcina pasteurii DSM33 for growth improvement in chemically defined and complex media. Sci Rep 2020; 10:22448. [PMID: 33384450 PMCID: PMC7775470 DOI: 10.1038/s41598-020-79904-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/10/2020] [Indexed: 11/12/2022] Open
Abstract
Microbial induced calcite precipitation (MICP) based on ureolysis has a high potential for many applications, e.g. restoration of construction materials. The gram-positive bacterium Sporosarcina pasteurii is the most commonly used microorganism for MICP due to its high ureolytic activity. However, Sporosarcina pasteurii is so far cultivated almost exclusively in complex media, which only results in moderate biomass concentrations at the best. Cultivation of Sporosarcina pasteurii must be strongly improved in order to make technological application of MICP economically feasible. The growth of Sporosarcina pasteurii DSM 33 was boosted by detecting auxotrophic deficiencies (L-methionine, L-cysteine, thiamine, nicotinic acid), nutritional requirements (phosphate, trace elements) and useful carbon sources (glucose, maltose, lactose, fructose, sucrose, acetate, L-proline, L-alanine). These were determined by microplate cultivations with online monitoring of biomass in a chemically defined medium and systematically omitting or substituting medium components. Persisting growth limitations were also detected, allowing further improvement of the chemically defined medium by the addition of glutamate group amino acids. Common complex media based on peptone and yeast extract were supplemented based on these findings. Optical density at the end of each cultivation of the improved peptone and yeast extract media roughly increased fivefold respectively. A maximum OD600 of 26.6 ± 0.7 (CDW: 17.1 ± 0.5 g/L) was reached with the improved yeast extract medium. Finally, culture performance and media improvement was analysed by measuring the oxygen transfer rate as well as the backscatter during shake flask cultivation.
Collapse
Affiliation(s)
| | - Jakob Schmid
- Munich University of Applied Sciences, 80335, Munich, Germany
| | - Benjamin Ederer
- Munich University of Applied Sciences, 80335, Munich, Germany
| | - Nina Ihling
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Robert Huber
- Munich University of Applied Sciences, 80335, Munich, Germany
| |
Collapse
|
22
|
Zhang W, Wang Y, Li K, Kwok LY, Liu W, Zhang H. Short communication: Modulation of fatty acid metabolism improves oxygen tolerance of Bifidobacterium animalis ssp. lactis Probio-M8. J Dairy Sci 2020; 103:8791-8795. [PMID: 32861486 DOI: 10.3168/jds.2019-18049] [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] [Received: 12/12/2019] [Accepted: 04/12/2020] [Indexed: 12/29/2022]
Abstract
Bifidobacterium animalis ssp. lactis Probio-M8 is a potential probiotic strain that was isolated from human milk. Previously, we obtained an oxygen-resistant variant (Probio-M8o) of Probio-M8 by an adaptive evolution strategy. In the present study, a comparative transcriptomic analysis of Probio-M8o and Probio-M8 was carried out to reveal the cellular mechanism of the oxygen-resistant phenotype. Using RNA-seq, 210 and 217 differentially expressed genes were identified in Probio-M8o compared with Probio-M8 after oxygen exposure for 30 and 60 min, respectively. The oxygen treatment upregulated a set of genes that encoded proteins responsible for fatty acid biosynthesis. This observation was in good agreement with the composition change in fatty acids at the biochemical level. Our study showed that the oxygen-resistant phenotype could be related to adaptation of fatty acid metabolism.
Collapse
Affiliation(s)
- Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Yuanchi Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Kangning Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China.
| |
Collapse
|
23
|
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.
Collapse
|
24
|
Turroni F, Milani C, Duranti S, Lugli GA, Bernasconi S, Margolles A, Di Pierro F, van Sinderen D, Ventura M. The infant gut microbiome as a microbial organ influencing host well-being. Ital J Pediatr 2020; 46:16. [PMID: 32024556 PMCID: PMC7003403 DOI: 10.1186/s13052-020-0781-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut.
Collapse
Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA - CSIC, Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
| |
Collapse
|
25
|
Sadiq FA, Yan B, Zhao J, Zhang H, Chen W. Untargeted metabolomics reveals metabolic state of Bifidobacterium bifidum in the biofilm and planktonic states. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108772] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
26
|
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models. Sci Rep 2019; 9:18222. [PMID: 31796826 PMCID: PMC6890778 DOI: 10.1038/s41598-019-54696-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/13/2019] [Indexed: 12/17/2022] Open
Abstract
Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.
Collapse
|
27
|
Turroni F, Duranti S, Milani C, Lugli GA, van Sinderen D, Ventura M. Bifidobacterium bifidum: A Key Member of the Early Human Gut Microbiota. Microorganisms 2019; 7:microorganisms7110544. [PMID: 31717486 PMCID: PMC6920858 DOI: 10.3390/microorganisms7110544] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/29/2019] [Accepted: 11/07/2019] [Indexed: 12/30/2022] Open
Abstract
Bifidobacteria typically represent the most abundant bacteria of the human gut microbiota in healthy breast-fed infants. Members of the Bifidobacterium bifidum species constitute one of the dominant taxa amongst these bifidobacterial communities and have been shown to display notable physiological and genetic features encompassing adhesion to epithelia as well as metabolism of host-derived glycans. In the current review, we discuss current knowledge concerning particular biological characteristics of the B. bifidum species that support its specific adaptation to the human gut and their implications in terms of supporting host health.
Collapse
Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
- Correspondence:
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland;
- APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
| |
Collapse
|
28
|
Bifidobacterial Transfer from Mother to Child as Examined by an Animal Model. Microorganisms 2019; 7:microorganisms7090293. [PMID: 31461893 PMCID: PMC6780879 DOI: 10.3390/microorganisms7090293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/12/2023] Open
Abstract
Bifidobacteria commonly constitute the most abundant group of microorganisms in the healthy infant gut. Their intestinal establishment is believed to be maternally driven, and their acquisition has even been postulated to occur during pregnancy. In the current study, we evaluated bifidobacterial mother-to infant transmission events in a rat model by means of quantitative PCR (qPCR), as well as by Internally Transcribed Spacer (ITS) bifidobacterial profiling. The occurrence of strains supplied by mothers during pregnancy to their corresponding newborns was observed and identified by analysis immediately following C-section delivery. These findings provide intriguing support for the existence of an unknown route to facilitate bifidobacterial transfer during the very early stages of life.
Collapse
|
29
|
Yang Y, Kumrungsee T, Kuroda M, Yamaguchi S, Kato N. Feeding Aspergillus protease preparation combined with adequate protein diet to rats increases levels of cecum gut-protective amino acids, partially linked to Bifidobacterium and Lactobacillus. Biosci Biotechnol Biochem 2019; 83:1901-1911. [PMID: 31181987 DOI: 10.1080/09168451.2019.1627183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Our recent study indicated that dietary Aspergillus oryzae-derived protease preparation (AP), through its enzymatic activity, exerted a bifidogenic effect in rats. We hypothesized that dietary AP links to protein degradation and subsequently elevates gut-protective amino acids (AAs) in rats fed adequate protein diet. In this study, dietary AP markedly increased the relative abundance of Bifidobacterium and Lactobacillus and the levels of free threonine, alanine, proline, taurine, ornithine, phenylalanine, cystine, and γ-aminobutyric acid in the cecum contents of rats fed with an adequate protein diet, but not in those fed with a low-protein diet. The elevated AAs, except ornithine and phenylalanine, potentially have gut-related health benefits. Some of the AP-modulated free AAs appeared to be associated with the relative abundance of Bifidobacterium and Lactobacillus. Thus, AP combined with adequate protein diet is likely to increase the levels of cecum beneficial free AAs, which is partially associated with the relative abundance of the probiotics.
Collapse
Affiliation(s)
- Yongshou Yang
- Graduate School of Integrated Sciences for Life, Hiroshima University , Higashi-Hiroshima , Japan
| | - Thanutchaporn Kumrungsee
- Graduate School of Integrated Sciences for Life, Hiroshima University , Higashi-Hiroshima , Japan
| | | | | | - Norihisa Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University , Higashi-Hiroshima , Japan
| |
Collapse
|
30
|
Seifert A, Freilich S, Kashi Y, Livney YD. Protein‐oligosaccharide conjugates as novel prebiotics. POLYM ADVAN TECHNOL 2019. [DOI: 10.1002/pat.4658] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Adi Seifert
- Laboratory of Biopolymers for Food and Health, Department of Biotechnology and Food EngineeringTechnion – Israel Institute of Technology Haifa 3200003 Israel
| | - Shay Freilich
- Laboratory of Applied Genomics, Department of Biotechnology and Food EngineeringTechnion – Israel Institute of Technology Haifa 3200003 Israel
| | - Yechezkel Kashi
- Laboratory of Applied Genomics, Department of Biotechnology and Food EngineeringTechnion – Israel Institute of Technology Haifa 3200003 Israel
| | - Yoav D. Livney
- Laboratory of Biopolymers for Food and Health, Department of Biotechnology and Food EngineeringTechnion – Israel Institute of Technology Haifa 3200003 Israel
| |
Collapse
|
31
|
Malmuthuge N, Liang G, Griebel PJ, Guan LL. Taxonomic and Functional Compositions of the Small Intestinal Microbiome in Neonatal Calves Provide a Framework for Understanding Early Life Gut Health. Appl Environ Microbiol 2019; 85:e02534-18. [PMID: 30658973 PMCID: PMC6414372 DOI: 10.1128/aem.02534-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole-genome sequencing of the metagenome, aiming to understand the dynamics of microbial establishment during early life. Despite highly individualized microbial communities, we identified two distinct taxonomy-based clusters from the collective luminal microbiomes comprising a high level of either Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus-dominant ileal microbiomes had significantly lower abundances of Bacteroides, Prevotella, Roseburia, Ruminococcus, and Veillonella compared to the Bacteroides-dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus-dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides-dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of mitogen-activated protein kinase cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2% ± 0.1%) compared to the protein metabolism-dominant cluster (12.6% ± 5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium, which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves.IMPORTANCE Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding of the early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to developing dietary interventions to improve calf gut health. The use of a metagenome sequencing-based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the preweaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density, and the abundance of taxa and functions were observed. A correlation-based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.
Collapse
Affiliation(s)
- Nilusha Malmuthuge
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Guanxiang Liang
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Philip J Griebel
- School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Le Luo Guan
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
32
|
Fuc E, Złotkowska D, Stachurska E, Wróblewska B. Immunoreactive properties of α-casein and κ-casein: Ex vivo and in vivo studies. J Dairy Sci 2018; 101:10703-10713. [PMID: 30292554 DOI: 10.3168/jds.2018-14915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/21/2018] [Indexed: 01/28/2023]
Abstract
The aim of this study was to evaluate the ex vivo and in vivo studies immune potential of α- and κ-casein. Ex vivo, naïve mouse splenocytes were stimulated with α- or κ-casein. After 120 h of culture, the proliferation index (PI), determined by 3-(4,5 dimethylthiazol-2yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and carboxyfluorescein diacetate N-succinimidyl ester (CFSE) staining, did not vary for either antigen, suggesting similar ex vivo immunogenic potential of both casein fractions. In vivo, BALB/ccmdb mice were sensitized with α- or κ-casein and then gavaged with primary antigen. Mice immunized with α-casein had higher levels of IgG (216.33) and IgA (210.22) in serum at the end of the experiment compared with mice immunized with κ-casein (215 and 29.3 for IgG and IgA, respectively). The use of α-casein for mouse immunization and ex vivo lymphocyte stimulation resulted in higher concentrations of secreted cytokines (IL-4, IL-10) compared with κ-casein stimulation. This is consistent with increasing regulatory T cell (Treg) lymphocyte populations, independent of the antigen used for stimulation. In summary, the immunogenic potential of α- and κ-casein was similar. Humoral and cellular immune responses confirmed their strong, independent potential to induce B and T cells. We propose that the lymphocyte proliferation index be used as an initial screening for protein immunogenicity.
Collapse
Affiliation(s)
- Ewa Fuc
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Poland
| | - Dagmara Złotkowska
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Poland
| | - Emilia Stachurska
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Poland
| | - Barbara Wróblewska
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, Poland.
| |
Collapse
|
33
|
Sharma V, Mobeen F, Prakash T. Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics. Genes (Basel) 2018; 9:genes9100477. [PMID: 30275399 PMCID: PMC6210967 DOI: 10.3390/genes9100477] [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: 08/25/2018] [Accepted: 09/10/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.
Collapse
Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| |
Collapse
|
34
|
Sarkar I, Tisa LS, Gtari M, Sen A. Biosynthetic energy cost of potentially highly expressed proteins vary with niche in selected actinobacteria. J Basic Microbiol 2017; 58:154-161. [PMID: 29144540 DOI: 10.1002/jobm.201700350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/27/2017] [Accepted: 11/05/2017] [Indexed: 11/08/2022]
Abstract
Amino acid and protein biosynthesis requires a number of high energy phosphate bonds and includes a dual energy cost for the synthesis of chemical intermediates during the fueling reactions and the conversion of precursor molecules to final products. One popular hypothesis is that the proteins encoded by putative highly expressed genes (hence called PHXPs) generally utilize low energy consuming amino acids to reduce the biosynthetic cost of the essential proteins. In our study, we found that this idea was not supported in the case of actinobacteria. With the actinobacteria, the energy costs of PHXPs varied in relation to their niche. Free-living, including aquatic, soil and extremophilic, and plant-associated actinobacteria were found to use energetically expensive amino acids in their PHXPs. An exception occurred with some animal-host-associated actinobacteria that used energy efficient amino acids. One explanation for these results may be due to the diverse metabolic patterns exhibited by actinobacteria under varied niches influenced by nutritional availability and physical environment.
Collapse
Affiliation(s)
- Indrani Sarkar
- NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, India
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis Elmanar (FST), Université de Carthage (INSAT), Tunis, Tunisia
| | - Arnab Sen
- NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, India
| |
Collapse
|
35
|
Portune KJ, Beaumont M, Davila AM, Tomé D, Blachier F, Sanz Y. Gut microbiota role in dietary protein metabolism and health-related outcomes: The two sides of the coin. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.08.011] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|