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Liu Y, Angelov A, Übelacker M, Baudrexl M, Ludwig C, Rühmann B, Sieber V, Liebl W. Proteomic analysis of Viscozyme L and its major enzyme components for pectic substrate degradation. Int J Biol Macromol 2024; 266:131309. [PMID: 38580019 DOI: 10.1016/j.ijbiomac.2024.131309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Enzymatic degradation of plant biomass requires the coordinated action of various enzymes. In this study, the production of reducing sugars from pectic substrates and sugar beet pulp (SBP) was investigated and compared using commercial enzyme preparations, including M2, pectinase (E1), Viscozyme L (V-L) and L-40. V-L, a cellulolytic enzyme mix produced by Aspergillus sp. was further evaluated as the most robust enzyme cocktail with the strongest SBP degradation ability in terms of the release of monosaccharides, methanol, and acetate from SBP. Mass-spectrometry-based proteomics analysis of V-L revealed 156 individual proteins. Of these, 101 proteins were annotated as containing a carbohydrate-active enzyme module. Notably, of the 50 most abundant proteins, ca. 44 % were predicted to be involved in pectin degradation. To reveal the role of individual putative key enzymes in pectic substrate decomposition, two abundant galacturonases (PglA and PglB), were heterologously expressed in Pichia pastoris and further characterized. PglA and PglB demonstrated maximum activity at 57 °C and 68 °C, respectively, and exhibited endo-type cleavage patterns towards polygalacturonic acid. Further studies along this line may lead to a better understanding of efficient SBP degradation and may help to design improved artificial enzyme mixtures with lower complexity for future application in biotechnology.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Maria Übelacker
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany.
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2
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Farooq A, Lee M, Han S, Jung GY, Kim SJ, Jung MY. Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces. Microbiol Spectr 2023; 11:e0504822. [PMID: 37707449 PMCID: PMC10581053 DOI: 10.1128/spectrum.05048-22] [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: 12/13/2022] [Accepted: 07/31/2023] [Indexed: 09/15/2023] Open
Abstract
Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.
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Affiliation(s)
- Adeel Farooq
- Research Institute for Basic Sciences (RIBS), Jeju National University, Jeju, South Korea
| | - Myunglip Lee
- Department of Marine Life Science, Jeju National University, Jeju, South Korea
| | - Saem Han
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Gi-Yong Jung
- Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, South Korea
| | - So-Jeong Kim
- Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
- Department of Science Education, Jeju National University, Jeju, South Korea
- Jeju Microbiome Center, Jeju National University, Jeju, South Korea
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3
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Frolova MS, Suvorova IA, Iablokov SN, Petrov SN, Rodionov DA. Genomic reconstruction of short-chain fatty acid production by the human gut microbiota. Front Mol Biosci 2022; 9:949563. [PMID: 36032669 PMCID: PMC9403272 DOI: 10.3389/fmolb.2022.949563] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
Short-chain fatty acids (SCFAs) including acetate, formate, propionate, and butyrate are the end products of dietary fiber and host glycan fermentation by the human gut microbiota (HGM). SCFAs produced in the column are of utmost importance for host physiology and health. Butyrate and propionate improve gut health and play a key role in the neuroendocrine and immune systems. Prediction of HGM metabolic potential is important for understanding the influence of diet and HGM-produced metabolites on human health. We conducted a detailed metabolic reconstruction of pathways for the synthesis of SCFAs and L- and D-lactate, as additional fermentation products, in a reference set of 2,856 bacterial genomes representing strains of >800 known HGM species. The reconstructed butyrate and propionate pathways included four and three pathway variants, respectively, that start from different metabolic precursors. Altogether, we identified 48 metabolic enzymes, including five alternative enzymes in propionate pathways, and propagated their occurrences across all studied genomes. We established genomic signatures for reconstructed pathways and classified genomes according to their simplified binary phenotypes encoding the ability (“1”) or inability (“0”) of a given organism to produce SCFAs. The resulting binary phenotypes combined into a binary phenotype matrix were used to assess the SCFA synthesis potential of HGM samples from several public metagenomic studies. We report baseline and variance for Community Phenotype Indices calculated for SCFAs production capabilities in 16S metagenomic samples of intestinal microbiota from two large national cohorts (American Gut Project, UK twins), the Hadza hunter-gatherers, and the young children cohort of infants with high-risk for type 1 diabetes. We further linked the predicted SCFA metabolic capabilities with available SCFA concentrations both for in vivo fecal samples and in vitro fermentation samples from previous studies. Finally, we analyzed differential representation of individual SCFA pathway genes across several WGS metagenomic datasets. The obtained collection of SCFA pathway genes and phenotypes enables the predictive metabolic phenotype profiling of HGM datasets and enhances the in silico methodology to study cross-feeding interactions in the gut microbiomes.
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Affiliation(s)
- Maria S. Frolova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Inna A. Suvorova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Stanislav N. Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Sergei N. Petrov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- *Correspondence: Dmitry A. Rodionov,
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4
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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.
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5
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Rodionov DA, Rodionova IA, Rodionov VA, Arzamasov AA, Zhang K, Rubinstein GM, Tanwee TNN, Bing RG, Crosby JR, Nookaew I, Basen M, Brown SD, Wilson CM, Klingeman DM, Poole FL, Zhang Y, Kelly RM, Adams MWW. Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii. mSystems 2021; 6:e0134520. [PMID: 34060910 PMCID: PMC8579813 DOI: 10.1128/msystems.01345-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022] Open
Abstract
Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono- and oligosaccharides. Through metabolic engineering, ethanol and other industrially important end products can be produced. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species Caldicellulosiruptor saccharolyticus and Caldicellulosiruptor bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to 14 Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site experimental data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose. IMPORTANCE To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium. Guided by the findings here, a clearer picture of how C. bescii natively drives carbohydrate utilization is provided and strategies to engineer this bacterium for optimal conversion of lignocellulose to commercial products emerge.
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Affiliation(s)
- Dmitry A. Rodionov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Irina A. Rodionova
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Vladimir A. Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A. Arzamasov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Ke Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Gabriel M. Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Tania N. N. Tanwee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mirko Basen
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Biowissenschaften, Mikrobiologie, Universität Rostock, Rostock, Germany
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Charlotte M. Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- University of Otago, Dunedin, New Zealand
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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6
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Peterson CT, Iablokov SN, Uchitel S, Chopra D, Perez-Santiago J, Rodionov DA, Peterson SN. Community Metabolic Interactions, Vitamin Production and Prebiotic Potential of Medicinal Herbs Used for Immunomodulation. Front Genet 2021; 12:584197. [PMID: 33613632 PMCID: PMC7886795 DOI: 10.3389/fgene.2021.584197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Historically, the health benefits and immunomodulatory potential of medicinal herbs have been considered an intrinsic quality of the herb itself. We have hypothesized that the health benefits of medicinal herbs may be partially due to their prebiotic potential that alter gut microbiota leading to changes in short chain fatty acids and vitamin production or biotransformation of herb encoded molecules and secondary metabolites. Accumulating studies emphasize the relationship between the gut microbiota and host immune function. While largely unknown, these interactions are mediated by secreted microbial products that activate or repress a variety of immune cell types. Here we evaluated the effect of immunomodulatory, medicinal Ayurvedic herbs on gut microbiota in vitro using 16S rRNA sequencing to assess changes in community composition and functional potential. All immunomodulatory herbs displayed substantial prebiotic potential, targeting unique taxonomic groups. Application of genome reconstruction and analysis of biosynthetic capacity of herb selected communities suggests that many of the 11 herbs tested altered the community metabolism as the result of differential glycan harvest and sugar utilization and secreted products including multiple vitamins, butyrate, and propionate that may impact host physiology and immune function. Taken together, these results provide a useful framework for the further evaluation of these immunomodulatory herbs in vivo to maintain immune homeostasis or achieve desired regulation of immune components in the context of disease.
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Affiliation(s)
- Christine T Peterson
- Department of Family Medicine and Public Health, Center of Excellence for Research and Training in Integrative Health, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Stanislav N Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Department of Theoretical Physics, P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Sasha Uchitel
- Department of Biology, Washington University, St. Louis, MO, United States
| | - Deepak Chopra
- Department of Family Medicine and Public Health, Center of Excellence for Research and Training in Integrative Health, School of Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Ayurveda and Yoga Research, Chopra Foundation, Carlsbad, CA, United States
| | - Josue Perez-Santiago
- Puerto Rico Omic Center Genomics Core Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Scott N Peterson
- Puerto Rico Omic Center Genomics Core Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico.,Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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7
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Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV. Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases. Front Mol Biosci 2021; 7:603740. [PMID: 33537340 PMCID: PMC7848230 DOI: 10.3389/fmolb.2020.603740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is of utmost importance to human health. While a healthy microbiome can be represented by a variety of structures, its functional capacity appears to be more important. Gene content of the community can be assessed by “shotgun” metagenomics, but this approach is still too expensive. High-throughput amplicon-based surveys are a method of choice for large-scale surveys of links between microbiome, diseases, and diet, but the algorithms for predicting functional composition need to be improved to achieve good precision. Here we show how feature engineering based on microbial phenotypes, an advanced method for functional prediction from 16S rRNA sequencing data, improves identification of alterations of the gut microbiome linked to the disease. We processed a large collection of published gut microbial datasets of inflammatory bowel disease (IBD) patients to derive their community phenotype indices (CPI)—high-precision semiquantitative profiles aggregating metabolic potential of the community members based on genome-wide metabolic reconstructions. The list of selected metabolic functions included metabolism of short-chain fatty acids, vitamins, and carbohydrates. The machine-learning approach based on microbial phenotypes allows us to distinguish the microbiome profiles of healthy controls from patients with Crohn's disease and from ones with ulcerative colitis. The classifiers were comparable in quality to conventional taxonomy-based classifiers but provided new findings giving insights into possible mechanisms of pathogenesis. Feature-wise partial dependence plot (PDP) analysis of contribution to the classification result revealed a diversity of patterns. These observations suggest a constructive basis for defining functional homeostasis of the healthy human gut microbiome. The developed features are promising interpretable candidate biomarkers for assessing microbiome contribution to disease risk for the purposes of personalized medicine and clinical trials.
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Affiliation(s)
- Stanislav N Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Natalia S Klimenko
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana Shashkova
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Pavel S Novichkov
- PhenoBiome Inc., San Francisco, CA, United States.,Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexander V Tyakht
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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8
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Jones RB, Berger PK, Plows JF, Alderete TL, Millstein J, Fogel J, Iablokov SN, Rodionov DA, Osterman AL, Bode L, Goran MI. Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants. Gut Microbes 2020; 12:1813534. [PMID: 32887539 PMCID: PMC7524300 DOI: 10.1080/19490976.2020.1813534] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 02/03/2023] Open
Abstract
Infant formula feeding, compared with human milk, has been associated with development of a distinct infant gut microbiome, but no previous study has examined effects of formula with added sugars. This work examined differences in gut microbiota among 91 Hispanic infants who consumed human milk [at breast (BB) vs. pumped in bottle (BP)] and 2 kinds of infant formula [(traditional lactose-based (TF) vs. lactose-reduced with added sugar (ASF)]. At 1 and 6 months, infant stool was collected to characterize gut microbiota. At 6 months, mothers completed 24-hour dietary recalls and questionnaires to determine infant consumption of human milk (BB vs. BP) or formula (TF vs. ASF). Linear regression models were used to determine associations of milk consumption type and microbial features at 6 months. Infants in the formula groups exhibited a significantly more 'mature' microbiome than infants in the human milk groups with the most pronounced differences observed between the ASF vs. BB groups. In the ASF group, we observed reduced log-normalized abundance of Bifidobacteriaceae (TF-BB Mean Difference = -0.71, ASF-BB Mean Difference = -1.10), and increased abundance of Lachnospiraceae (TF-BB Mean Difference = +0.89, ASF-BB Mean Difference = +1.20). We also observed a higher Community Phenotype Index of propionate, most likely produced by Lachnospiraceae, in the ASF group (TF-BB Mean Difference = +0.27, ASF-BB Mean Difference = +0.36). This study provides the first evidence that consumption of infant formula with added sugar may have a stronger association than birth delivery mode, infant caloric intake, and maternal BMI on the infant's microbiome at 6 months of age.
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Affiliation(s)
- Roshonda B. Jones
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Paige K. Berger
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Jasmine F. Plows
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Joshua Millstein
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jennifer Fogel
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Stanislav N. Iablokov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Dmitry A. Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California, San Diego, CA, USA
| | - Michael I. Goran
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
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9
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Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments. Nat Commun 2020; 11:3135. [PMID: 32561713 PMCID: PMC7305145 DOI: 10.1038/s41467-020-16872-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
It is commonly thought that when multiple carbon sources are available, bacteria metabolize them either sequentially (diauxic growth) or simultaneously (co-utilization). However, this view is mainly based on analyses in relatively simple laboratory settings. Here we show that a heterotrophic marine bacterium, Pseudoalteromonas haloplanktis, can use both strategies simultaneously when multiple possible nutrients are provided in the same growth experiment. The order of nutrient uptake is partially determined by the biomass yield that can be achieved when the same compounds are provided as single carbon sources. Using transcriptomics and time-resolved intracellular 1H-13C NMR, we reveal specific pathways for utilization of various amino acids. Finally, theoretical modelling indicates that this metabolic phenotype, combining diauxie and co-utilization of substrates, is compatible with a tight regulation that allows the modulation of assimilatory pathways. It is thought that when multiple carbon sources are available, bacteria metabolize them either sequentially or simultaneously. Here, the authors show that a marine bacterium can use a mixed strategy when multiple possible nutrients are provided, and analyse the metabolic pathways involved.
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Rijavec T, Zrimec J, van Spanning R, Lapanje A. Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1901408. [PMID: 31763146 PMCID: PMC6865284 DOI: 10.1002/advs.201901408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Biofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC-related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water-proof rubber elastomer barrier. The artificial biofilm is constructed layer-by-layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular-biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC-related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.
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Affiliation(s)
- Tomaž Rijavec
- Department of Environmental SciencesJožef Stefan InstituteJamova cesta 391000LjubljanaSlovenia
- Institute of Metagenomics and Microbial TechnologiesClevelandska ulica 191000LjubljanaSlovenia
| | - Jan Zrimec
- Institute of Metagenomics and Microbial TechnologiesClevelandska ulica 191000LjubljanaSlovenia
- Systems and Synthetic BiologyChalmers University of TechnologyKemivägen 10412 96GöteborgSweden
| | - Rob van Spanning
- Systems BioinformaticsFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 11051081 HVAmsterdamThe Netherlands
| | - Aleš Lapanje
- Department of Environmental SciencesJožef Stefan InstituteJamova cesta 391000LjubljanaSlovenia
- Institute of Metagenomics and Microbial TechnologiesClevelandska ulica 191000LjubljanaSlovenia
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11
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Zhou G, Qiu X, Zhang J, Tao C. Effects of seaweed fertilizer on enzyme activities, metabolic characteristics, and bacterial communities during maize straw composting. BIORESOURCE TECHNOLOGY 2019; 286:121375. [PMID: 31030066 DOI: 10.1016/j.biortech.2019.121375] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/19/2019] [Accepted: 04/20/2019] [Indexed: 06/09/2023]
Abstract
The objective of this study was to investigate microbial responses when seaweed fertilizer was added to maize straw compost. The metabolic characteristics and bacterial communities were assessed using 16S rRNA sequencing and Biolog analysis. Results showed that the urease, dehydrogenase, and metabolic activities improved on day 21 after the addition of seaweed fertilizer. Firmicutes, Proteobacteria, and Actinobacteria were the dominant phyla in the compost. The relative abundances of Proteobacteria and Actinobacteria were increased by addition of seaweed fertilizer during the early composting stage. Temperature, NH4+-N, NO3--N concentrations, and carbon source metabolism had close relationships with bacterial community variation during composting. A network analysis revealed that NO3--N content had a positive association with Aeromicrobium, and seaweed fertilizer application improved the growth of keystone species related to N cycling. These results suggested that seaweed fertilizer influenced bacterial community succession through its effects on N concentrations during the composting process.
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Affiliation(s)
- Guixiang Zhou
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiuwen Qiu
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; Office of Mountain-River-Lake Development Committee of Jiangxi Province, Nanchang 330046, China.
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunyuan Tao
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China
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12
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Genome analysis provides insights into crude oil degradation and biosurfactant production by extremely halotolerant Halomonas desertis G11 isolated from Chott El-Djerid salt-lake in Tunisian desert. Genomics 2018; 111:1802-1814. [PMID: 30529640 DOI: 10.1016/j.ygeno.2018.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/05/2018] [Accepted: 12/04/2018] [Indexed: 01/10/2023]
Abstract
Here, we report the genomic features and the bioremediation potential of Halomonas desertis G11, a new halophilic species which uses crude oil as a carbon and energy source and displays intrinsic resistance to salt stress conditions (optimum growth at 10% NaCl). G11 genome (3.96 Mb) had a mean GC content of 57.82%, 3622 coding sequences, 480 subsystems and 64 RNA genes. Annotation predicted 38 genes involved in osmotic stress including the biosynthesis of osmoprotectants glycine-betaine, ectoine and osmoregulated periplasmic glucans. Genome analysis revealed also the versatility of the strain for emulsifying crude oil and metabolizing hydrocarbons. The ability of G11 to degrade crude oil components and to secrete a glycolipid biosurfactant with satisfying properties was experimentally confirmed and validated. Our results help to explain the exceptional capacity of G11 to survive at extreme desertic conditions, and highlight the metabolic features of this organism that has biotechnological and ecological potentialities.
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13
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White RA, Gavelis G, Soles SA, Gosselin E, Slater GF, Lim DSS, Leander B, Suttle CA. The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress. Front Microbiol 2018; 9:2180. [PMID: 30374333 PMCID: PMC6196244 DOI: 10.3389/fmicb.2018.02180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 08/24/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the bacterial genus Agrococcus are globally distributed and found across environments so highly diverse that they include forests, deserts, and coal mines, as well as in potatoes and cheese. Despite how widely Agrococcus occurs, the extent of its physiology, genomes, and potential roles in the environment are poorly understood. Here we use whole-genome analysis, chemotaxonomic markers, morphology, and 16S rRNA gene phylogeny to describe a new isolate of the genus Agrococcus from freshwater microbialites in Pavilion Lake, British Columbia, Canada. We characterize this isolate as a new species Agrococcus pavilionensis strain RW1 and provide the first complete genome from a member of the genus Agrococcus. The A. pavilionensis genome consists of one chromosome (2,627,177 bp) as well as two plasmids (HC-CG1 1,427 bp, and LC-RRW783 31,795 bp). The genome reveals considerable genetic promiscuity via mobile elements, including a prophage and plasmids involved in integration, transposition, and heavy-metal stress. A. pavilionensis strain RW1 differs from other members of the Agrococcus genus by having a novel phospholipid fatty acid iso-C15:1Δ4, β-galactosidase activity and amygdalin utilization. Carotenoid biosynthesis is predicted by genomic metabolic reconstruction, which explains the characteristic yellow pigmentation of A. pavilionensis. Metabolic reconstructions of strain RW1 genome predicts a pathway for releasing ammonia via ammonification amino acids, which could increase the saturation index leading to carbonate precipitation. Our genomic analyses suggest signatures of environmental adaption to the relatively cold and oligotrophic conditions of Pavilion Lake microbialites. A. pavilionensis strain RW1 in modern microbialites has an ecological significance in Pavilion Lake microbialites, which include potential roles in heavy-metal cycling and carbonate precipitation (e.g., ammonification of amino acids and filamentation which many trap carbonate minerals).
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Affiliation(s)
- Richard Allen White
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Greg Gavelis
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Sarah A Soles
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Emma Gosselin
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Greg F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Darlene S S Lim
- Bay Area Environmental Research Institute, Petaluma, CA, United States.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Brian Leander
- Bay Area Environmental Research Institute, Petaluma, CA, United States
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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14
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Rosa LT, Bianconi ME, Thomas GH, Kelly DJ. Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity. Front Cell Infect Microbiol 2018; 8:33. [PMID: 29479520 PMCID: PMC5812351 DOI: 10.3389/fcimb.2018.00033] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/25/2018] [Indexed: 11/18/2022] Open
Abstract
The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. All catabolic pathways must begin with the transport of substrate from the environment through the cytoplasmic membrane, a role executed by membrane transporters. Although several classes of cytoplasmic membrane transporters are described, high-affinity uptake of substrates occurs through Solute Binding-Protein (SBP) dependent systems. Three families of SBP dependant transporters are known; the primary ATP-binding cassette (ABC) transporters, and the secondary Tripartite ATP-independent periplasmic (TRAP) transporters and Tripartite Tricarboxylate Transporters (TTT). Far less well understood than the ABC family, the TRAP transporters are found to be abundant among bacteria from marine environments, and the TTT transporters are the most abundant family of proteins in many species of β-proteobacteria. In this review, recent knowledge about these families is covered, with emphasis on their physiological and structural mechanisms, relating to several examples of relevant uptake systems in pathogenicity and colonization, using the SiaPQM sialic acid uptake system from Haemophilus influenzae and the TctCBA citrate uptake system of Salmonella typhimurium as the prototypes for the TRAP and TTT transporters, respectively. High-throughput analysis of SBPs has recently expanded considerably the range of putative substrates known for TRAP transporters, while the repertoire for the TTT family has yet to be fully explored but both types of systems most commonly transport carboxylates. Specialized spectroscopic techniques and site-directed mutagenesis have enriched our knowledge of the way TRAP binding proteins capture their substrate, while structural comparisons show conserved regions for substrate coordination in both families. Genomic and protein sequence analyses show TTT SBP genes are strikingly overrepresented in some bacteria, especially in the β-proteobacteria and some α-proteobacteria. The reasons for this are not clear but might be related to a role for these proteins in signaling rather than transport.
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Affiliation(s)
- Leonardo T Rosa
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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15
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Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture. Sci Rep 2018; 8:297. [PMID: 29321512 PMCID: PMC5762899 DOI: 10.1038/s41598-017-18630-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/14/2017] [Indexed: 01/09/2023] Open
Abstract
The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.
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16
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Ji ZH, Ren WZ, Gao W, Hao Y, Gao W, Chen J, Quan FS, Hu JP, Yuan B. Analyzing the innate immunity of NIH hairless mice and the impact of gut microbial polymorphisms on Listeria monocytogenes infection. Oncotarget 2017; 8:106222-106232. [PMID: 29290943 PMCID: PMC5739728 DOI: 10.18632/oncotarget.22051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/03/2017] [Indexed: 12/12/2022] Open
Abstract
Spontaneous mutant hairless (HL) mice are often used to study hair growth and hair follicle development, and they often exhibit immune dysfunctions. Listeria monocytogenes, an important food-borne bacterium, has been used in animal models to study immune responses to infection. Herein, we analyzed the innate immunity of HL mice and the impact of gut microbial polymorphisms on L. monocytogenes infection. Compared to NIH mice, NIH HL mice were more susceptible to L. monocytogenes, as weight losses, mortality, bacterial load, and histopathological lesions were more severe; the decrease in monocytes may be an important underlying reason. The degree of spleen damage was reduced after co-housing, indicating that the host guides the gut microbiota to alleviate infection. High-throughput pyrosequencing of 16S rRNA demonstrated that gut microbiota composition differed between NIH HL and NIH mice. Infection with L. monocytogenes induced an increase in the number of bacteria belonging to the Rikenellaceae family and Gammaproteobacteria class, and decreased bacteria belonging to the Clostridiales class and Lachnospiraceae family. A substantial reduction in Clostridiales bacteria in infected HL mice may cause a serious infection. The Mycoplasma genus was present only in NIH HL mice and was, thus, considered a biomarker. The results of this study improve our understanding of the use of NIH HL mice as a good animal model of innate immune dysfunction.
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Affiliation(s)
- Zhong-Hao Ji
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Wen-Zhi Ren
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Wei Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Yang Hao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Wei Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Jian Chen
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Fu-Shi Quan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Jin-Ping Hu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
| | - Bao Yuan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China
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