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Galichet C, Rizzoti K, Lovell-Badge R. Hypopituitarism in Sox3 null mutants correlates with altered NG2-glia in the median eminence and is influenced by aspirin and gut microbiota. PLoS Genet 2024; 20:e1011395. [PMID: 39325695 PMCID: PMC11426531 DOI: 10.1371/journal.pgen.1011395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 08/13/2024] [Indexed: 09/28/2024] Open
Abstract
The median eminence (ME), located at the base of the hypothalamus, is an essential centre of information exchange between the brain and the pituitary. We and others previously showed that mutations and duplications affecting the transcription factor SOX3/Sox3 result in hypopituitarism, and this is likely of hypothalamic origin. We demonstrate here that the absence of Sox3 predominantly affects the ME with phenotypes that first occur in juvenile animals, despite the embryonic onset of SOX3 expression. In the pituitary, reduction in hormone levels correlates with a lack of endocrine cell maturation. In parallel, ME NG2-glia renewal and oligodendrocytic differentiation potential are affected. We further show that low-dose aspirin treatment, which is known to affect NG2-glia, or changes in gut microbiota, rescue both proliferative defects and hypopituitarism in Sox3 mutants. Our study highlights a central role of NG2-glia for ME function during a transitional period of post-natal development and indicates their sensitivity to extrinsic signals.
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Affiliation(s)
- Christophe Galichet
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
- Neurobiological Research Facility, UCL Sainsbury Wellcome Centre for Neural Circuits and Behaviour, London, United Kingdom
| | - Karine Rizzoti
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
| | - Robin Lovell-Badge
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
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2
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Wang X, Wang Z, Su S, Wu Y, Fan J, Hou X, Zhang K, Salama ES, Kulshrestha S, Ling Z, Liu P, Li X. Probiotics Pediococcus acidilactici GR-1 promotes the functional strains and remodels gut microbiota to reduce the Cr(VI) toxicity in a dual-chamber simulated intestinal system. CHEMOSPHERE 2024; 356:141927. [PMID: 38593954 DOI: 10.1016/j.chemosphere.2024.141927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/29/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Abstract
Numerous animal studies have demonstrated the toxicity of hexavalent chromium [Cr(VI)] and the bioremediative effects of probiotics on the composition and functions of gut microbiota. Since the precise mechanisms of Cr(VI) detoxification and its interactions with human gut microbiota were unknown, a novel dual-chamber simulated intestinal (DCSI) system was developed to maintain both the stability of the simulated system and the composition of the gut microbiota. Probiotic GR-1 was found to regulate intestinal gut microbiota, thereby reducing the toxicity of Cr(VI) within the DCSI system. The results indicate that Cr(VI) levels were reduced from 2.260 ± 0.2438 μg/g to 1.7086 ± 0.1950 μg/g in the gut microbiota cell pellet, and Cr(VI) permeability decreased from 0.5521 ± 0.1132 μg/L to 0.3681 ± 0.0178 μg/L after 48 h in simulated gut fluid. Additionally, the removal rate of 1,1-Diphenyl-2-picrylhydrazyl (DPPH), reducibility (Vitamin C), and total antioxidant capacity (T-AOC) increased by 50.83%, 31.70%, and 27.56%, respectively, following probiotic treatment. The increase in antioxidant capacity correlated with total Cr removal (P < 0.05, r from -0.80 to 0.73). 16S rRNA sequencing analysis showed that gut microbiota composition was reshaped by the addition of probiotics, which regulated the recovery of the functional gut microbiota to normal levels, rather than restoring the entire gut microbiota composition for community function. Thus, this study not only demonstrates the feasibility and stability of culturing gut microbiota but also offers a new biotechnological approach to synthesizing functional communities with functional strains for environmental risk management.
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Affiliation(s)
- Xing Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Zemin Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Shaochen Su
- Healthy Examination & Management Center, First Hospital of Lanzhou University, Lanzhou, 730000, PR China.
| | - Ying Wu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Jingjing Fan
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Xiaoxiao Hou
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Kunyue Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China.
| | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Biotechnology and Management Sciences, Shoolini University, Bajhol, Solan, Himachal Pradesh, 173229, India.
| | - Zhenmin Ling
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Pu Liu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Xiangkai Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
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3
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Angima G, Qu Y, Park SH, Dallas DC. Prebiotic Strategies to Manage Lactose Intolerance Symptoms. Nutrients 2024; 16:1002. [PMID: 38613035 PMCID: PMC11013211 DOI: 10.3390/nu16071002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Lactose intolerance, which affects about 65-75% of the world's population, is caused by a genetic post-weaning deficiency of lactase, the enzyme required to digest the milk sugar lactose, called lactase non-persistence. Symptoms of lactose intolerance include abdominal pain, bloating and diarrhea. Genetic variations, namely lactase persistence, allow some individuals to metabolize lactose effectively post-weaning, a trait thought to be an evolutionary adaptation to dairy consumption. Although lactase non-persistence cannot be altered by diet, prebiotic strategies, including the consumption of galactooligosaccharides (GOSs) and possibly low levels of lactose itself, may shift the microbiome and mitigate symptoms of lactose consumption. This review discusses the etiology of lactose intolerance and the efficacy of prebiotic approaches like GOSs and low-dose lactose in symptom management.
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Affiliation(s)
- Gloria Angima
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (G.A.); (Y.Q.)
| | - Yunyao Qu
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (G.A.); (Y.Q.)
- Nutrition Program, School of Nutrition and Public Health, College of Health, Oregon State University, Corvallis, OR 97331, USA
| | - Si Hong Park
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (G.A.); (Y.Q.)
| | - David C. Dallas
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (G.A.); (Y.Q.)
- Nutrition Program, School of Nutrition and Public Health, College of Health, Oregon State University, Corvallis, OR 97331, USA
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Zhao H, Li S, Pu J, Wang H, Dou X. Effects of Bacillus-based inoculum on odor emissions co-regulation, nutrient element transformations and microbial community tropological structures during chicken manure and sawdust composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120328. [PMID: 38354615 DOI: 10.1016/j.jenvman.2024.120328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/16/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
This study aims to evaluate whether different doses of Bacillus-based inoculum inoculated in chicken manure and sawdust composting will provide distinct effects on the co-regulation of ammonia (NH3) and hydrogen sulfide (H2S), nutrient conversions and microbial topological structures. Results indicate that the Bacillus-based inoculum inhibits NH3 emissions mainly by regulating bacterial communities, while promotes H2S emissions by regulating both bacterial and fungal communities. The inoculum only has a little effect on total organic carbon (TOC) and inhibits total sulfur (TS) and total phosphorus (TP) accumulations. Low dose inoculation inhibits total potassium (TK) accumulation, while high dose inoculation promotes TK accumulation and the opposite is true for total nitrogen (TN). The inoculation slightly affects the bacterial compositions, significantly alters the fungal compositions and increases the microbial cooperation, thus influencing the compost substances transformations. The microbial communities promote ammonium nitrogen (NH4+-N), TN, available phosphorus (AP), total potassium (TK) and TS, but inhibit nitrate nitrogen (NO3--N), TP and TK. Additionally, the bacterial communities promote, while the fungal communities inhibit the nitrite nitrogen (NO2--N) production. The core bacterial and fungal genera regulate NH3 and H2S emissions through the secretions of metabolic enzymes and the promoting or inhibiting effects on NH3 and H2S emissions are always opposite. Hence, Bacillus-based inoculum cannot regulate the NH3 and H2S emissions simultaneously.
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Affiliation(s)
- Huaxuan Zhao
- Jiangsu Institute of Poultry Sciences, Yangzhou, 225125, China
| | - Shangmin Li
- Jiangsu Institute of Poultry Sciences, Yangzhou, 225125, China.
| | - Junhua Pu
- Jiangsu Institute of Poultry Sciences, Yangzhou, 225125, China
| | - Hongzhi Wang
- Jiangsu Institute of Poultry Sciences, Yangzhou, 225125, China
| | - Xinhong Dou
- Jiangsu Institute of Poultry Sciences, Yangzhou, 225125, China
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Li L, Li S, Luo J, Chen T, Xi Q, Zhang Y, Sun J. The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets. BMC Vet Res 2023; 19:174. [PMID: 37759242 PMCID: PMC10523759 DOI: 10.1186/s12917-023-03642-z] [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: 11/15/2022] [Accepted: 07/12/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The early development of intestinal microbiota plays a fundamental role in host health and development. To investigate the difference in the intestinal microbial composition between Lantang and Landrace newborn piglets, we amplified and sequenced the V3-V4 region of 16 S rRNA gene in jejunal microbiota of Lantang and landrace newborn. RESULTS The findings revealed that the dominant phyla in the jejunum of Lantang piglets were Firmicutes, Actinobacteria and Bacteroidetes, while the dominant phyla of Landrace is Proteobacteria and Fusobacteria. Specifically, Corynebacterium_1, Lactobacillus, Rothia, Granulicatella, Corynebacteriales_unclassified, Corynebacterium, Globicatella and Actinomycetales_unclassified were found to be the dominant genera of Lantang group, while Clostridium_sensu_stricto_1, Escherichia-Shigella, Actinobacillus and Bifidobacterium were the dominant genera of Landrace. Based on the functional prediction of bacteria, we found that bacterial communities from Lantang samples had a significantly greater abundance pathways of fatty acid synthesis, protein synthesis, DNA replication, recombination, repair and material transport across membranes, while the carrier protein of pathogenic bacteria was more abundant in Landrace samples. CONCLUSIONS Overall, there was a tremendous difference in the early intestinal flora composition between Landang and Landrace piglets, which was related to the breed characteristics and may be one of the reasons affecting the growth characteristics. However, more further extensive studies should be included to reveal the underlying relationship between early intestinal flora composition in different breeds and pig growth characteristics.
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Affiliation(s)
- Ling Li
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Shuai Li
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Junyi Luo
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ting Chen
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qianyun Xi
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yongliang Zhang
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
| | - Jiajie Sun
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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Liu Y, Chen S, Wang J, Shao B, Fang J, Cao J. The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea. Microorganisms 2023; 11:2156. [PMID: 37764000 PMCID: PMC10536192 DOI: 10.3390/microorganisms11092156] [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: 08/08/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel Bacillota bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus Abyssisolibacter within the phylum Bacillota. Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535000, China
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China;
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Baoying Shao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
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Fu M, Cao Z, Sun R, Wen X, Wang Y, Li K, Li Q. Maleic anhydride promotes humus formation via inducing functional enzymes response in composting. BIORESOURCE TECHNOLOGY 2023; 380:129125. [PMID: 37127171 DOI: 10.1016/j.biortech.2023.129125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
The purpose of this paper was to explore the promotion of maleic anhydride on the polymerization of precursors into humus in composting, and analyze the changes of key functional enzymes. The results showed that the content of humus in the treatment group added maleic anhydride (MAH) was higher than that in the control check (CK). The decrease rate of humus precursor concentration of MAH was also higher than that of CK. In MAH, the activities of laccase and tyrosinase were improved, thus enhanced the catalytic conversion of humus precursors. The analysis of bacterial community showed that maleic anhydride optimized the community structure of humification functional enzymes producing bacteria, with the most obvious increase of Firmicutes. In conclusion, this study provided theoretical supports for the introduction of maleic anhydride into the compost system to promote the polymerization of precursors to form humus.
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Affiliation(s)
- Mengxin Fu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Ziyi Cao
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Ru Sun
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xiaoli Wen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yiwu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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8
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Firrman J, Liu L, Mahalak K, Hu W, Bittinger K, Moustafa A, Jones SM, Narrowe A, Tomasula P. An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner. Front Nutr 2023; 9:1040744. [PMID: 36778971 PMCID: PMC9908759 DOI: 10.3389/fnut.2022.1040744] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/14/2022] [Indexed: 01/27/2023] Open
Abstract
Introduction Following consumption of milk, lactose, a disaccharide of glucose and galactose, is hydrolyzed and absorbed in the upper gastrointestinal tract. However, hydrolysis and absorption are not always absolute, and some lactose will enter the colon where the gut microbiota is able to hydrolyze lactose and produce metabolic byproducts. Methods Here, the impact of lactose on the gut microbiota of healthy adults was examined, using a short-term, in vitro strategy where fecal samples harvested from 18 donors were cultured anaerobically with and without lactose. The data were compiled to identify donor-independent responses to lactose treatment. Results and discussion Metagenomic sequencing found that the addition of lactose decreased richness and evenness, while enhancing prevalence of the β-galactosidase gene. Taxonomically, lactose treatment decreased relative abundance of Bacteroidaceae and increased lactic acid bacteria, Lactobacillaceae, Enterococcaceae, and Streptococcaceae, and the probiotic Bifidobacterium. This corresponded with an increased abundance of the lactate utilizers, Veillonellaceae. These structural changes coincided with increased total short-chain fatty acids (SCFAs), specifically acetate, and lactate. These results demonstrated that lactose could mediate the gut microbiota of healthy adults in a donor-independent manner, consistent with other described prebiotics, and provided insight into how dietary milk consumption may promote human health through modifications of the gut microbiome.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States,*Correspondence: Jenni Firrman,
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
| | - Karley Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ahmed Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Adrienne Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
| | - Peggy Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
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9
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Miller RD, Iinishi A, Modaresi SM, Yoo BK, Curtis TD, Lariviere PJ, Liang L, Son S, Nicolau S, Bargabos R, Morrissette M, Gates MF, Pitt N, Jakob RP, Rath P, Maier T, Malyutin AG, Kaiser JT, Niles S, Karavas B, Ghiglieri M, Bowman SEJ, Rees DC, Hiller S, Lewis K. Computational identification of a systemic antibiotic for gram-negative bacteria. Nat Microbiol 2022; 7:1661-1672. [PMID: 36163500 PMCID: PMC10155127 DOI: 10.1038/s41564-022-01227-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Discovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an attractive target due to its surface location. Darobactins produced by Photorhabdus, a nematode gut microbiome symbiont, target BamA. We reasoned that a computational search for genes only distantly related to the darobactin operon may lead to novel compounds. Following this clue, we identified dynobactin A, a novel peptide antibiotic from Photorhabdus australis containing two unlinked rings. Dynobactin is structurally unrelated to darobactins, but also targets BamA. Based on a BamA-dynobactin co-crystal structure and a BAM-complex-dynobactin cryo-EM structure, we show that dynobactin binds to the BamA lateral gate, uniquely protruding into its β-barrel lumen. Dynobactin showed efficacy in a mouse systemic Escherichia coli infection. This study demonstrates the utility of computational approaches to antibiotic discovery and suggests that dynobactin is a promising lead for drug development.
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Affiliation(s)
- Ryan D Miller
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | | | - Byung-Kuk Yoo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas D Curtis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Patrick J Lariviere
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Libang Liang
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sangkeun Son
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Samantha Nicolau
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Rachel Bargabos
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Madeleine Morrissette
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Michael F Gates
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Norman Pitt
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | | | | | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
| | - Andrey G Malyutin
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Jens T Kaiser
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Samantha Niles
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Blake Karavas
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Sarah E J Bowman
- National Crystallization Center, Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | | | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.
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10
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Brettle H, Tran V, Drummond GR, Franks AE, Petrovski S, Vinh A, Jelinic M. Sex hormones, intestinal inflammation, and the gut microbiome: Major influencers of the sexual dimorphisms in obesity. Front Immunol 2022; 13:971048. [PMID: 36248832 PMCID: PMC9554749 DOI: 10.3389/fimmu.2022.971048] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Obesity is defined as the excessive accumulation of body fat and is associated with an increased risk of developing major health problems such as cardiovascular disease, diabetes and stroke. There are clear sexual dimorphisms in the epidemiology, pathophysiology and sequelae of obesity and its accompanying metabolic disorders, with females often better protected compared to males. This protection has predominantly been attributed to the female sex hormone estrogen and differences in fat distribution. More recently, the sexual dimorphisms of obesity have also been attributed to the differences in the composition and function of the gut microbiota, and the intestinal immune system. This review will comprehensively summarize the pre-clinical and clinical evidence for these sexual dimorphisms and discuss the interplay between sex hormones, intestinal inflammation and the gut microbiome in obesity. Major gaps and limitations of this rapidly growing area of research will also be highlighted in this review.
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Affiliation(s)
- Holly Brettle
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Vivian Tran
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Grant R. Drummond
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Ashley E. Franks
- Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Steve Petrovski
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Antony Vinh
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Maria Jelinic
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Maria Jelinic,
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11
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Keskitalo A, Munukka E, Aatsinki A, Saleem W, Kartiosuo N, Lahti L, Huovinen P, Elo LL, Pietilä S, Rovio SP, Niinikoski H, Viikari J, Rönnemaa T, Lagström H, Jula A, Raitakari O, Pahkala K. An Infancy-Onset 20-Year Dietary Counselling Intervention and Gut Microbiota Composition in Adulthood. Nutrients 2022; 14:2667. [PMID: 35807848 PMCID: PMC9268486 DOI: 10.3390/nu14132667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
The randomized controlled Special Turku Coronary Risk Factor Intervention Project (STRIP) has completed a 20-year infancy-onset dietary counselling intervention to reduce exposure to atherosclerotic cardiovascular disease risk factors via promotion of a heart-healthy diet. The counselling on, e.g., low intake of saturated fat and cholesterol and promotion of fruit, vegetable, and whole-grain consumption has affected the dietary characteristics of the intervention participants. By leveraging this unique cohort, we further investigated whether this long-term dietary intervention affected the gut microbiota bacterial profile six years after the intervention ceased. Our sub-study comprised 357 individuals aged 26 years (intervention n = 174, control n = 183), whose gut microbiota were profiled using 16S rRNA amplicon sequencing. We observed no differences in microbiota profiles between the intervention and control groups. However, out of the 77 detected microbial genera, the Veillonella genus was more abundant in the intervention group compared to the controls (log2 fold-change 1.58, p < 0.001) after adjusting for multiple comparison. In addition, an association between the study group and overall gut microbiota profile was found only in males. The subtle differences in gut microbiota abundances observed in this unique intervention setting suggest that long-term dietary counselling reflecting dietary guidelines may be associated with alterations in gut microbiota.
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Affiliation(s)
- Anniina Keskitalo
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland; (A.K.); (N.K.); (S.P.R.); (H.N.); (O.R.)
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
- Department of Clinical Microbiology, Turku University Hospital, 20520 Turku, Finland;
| | - Eveliina Munukka
- Microbiome Biobank, Institute of Biomedicine, University of Turku, 20520 Turku, Finland;
| | - Anna Aatsinki
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
| | - Wisam Saleem
- Department of Computing, Faculty of Technology, University of Turku, 20520 Turku, Finland; (W.S.); (L.L.)
| | - Noora Kartiosuo
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland; (A.K.); (N.K.); (S.P.R.); (H.N.); (O.R.)
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
- Department of Mathematics and Statistics, University of Turku, 20520 Turku, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, 20520 Turku, Finland; (W.S.); (L.L.)
| | - Pentti Huovinen
- Department of Clinical Microbiology, Turku University Hospital, 20520 Turku, Finland;
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland;
| | - Laura L. Elo
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland;
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland;
| | - Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland;
| | - Suvi P. Rovio
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland; (A.K.); (N.K.); (S.P.R.); (H.N.); (O.R.)
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
| | - Harri Niinikoski
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland; (A.K.); (N.K.); (S.P.R.); (H.N.); (O.R.)
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
- Department of Physiology/Department of Pediatrics, University of Turku, 20520 Turku, Finland
| | - Jorma Viikari
- Department of Medicine, University of Turku, 20520 Turku, Finland; (J.V.); (T.R.)
- Division of Medicine, Turku University Hospital, 20520 Turku, Finland
| | - Tapani Rönnemaa
- Department of Medicine, University of Turku, 20520 Turku, Finland; (J.V.); (T.R.)
- Division of Medicine, Turku University Hospital, 20520 Turku, Finland
| | - Hanna Lagström
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
- Department of Public Health, University of Turku and Turku University Hospital, 20520 Turku, Finland
| | - Antti Jula
- Department of Public Health Solutions, Institute for Health and Welfare, 20520 Turku, Finland;
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland; (A.K.); (N.K.); (S.P.R.); (H.N.); (O.R.)
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, University of Turku, 20520 Turku, Finland
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland; (A.K.); (N.K.); (S.P.R.); (H.N.); (O.R.)
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520 Turku, Finland; (A.A.); (H.L.)
- Paavo Nurmi Centre & Unit for Health and Physical Activity, University of Turku, 20520 Turku, Finland
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12
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Zhao H, Li S, Jiang Y, Wang D, Wang H, Dou X. Independent and combined effects of antibiotic stress and EM microbial agent on the nitrogen and humus transformation and bacterial community successions during the chicken manure composting. BIORESOURCE TECHNOLOGY 2022; 354:127237. [PMID: 35489576 DOI: 10.1016/j.biortech.2022.127237] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
This study aimed to investigate the independent and combined effects of antibiotic and EM microbial agent on the nitrogen and humus (HS) transformations as well as the bacterial community successions during the chicken manure and rice husk composting. EM microbial agent accelerated the oxytetracycline (OTC) degradation, but slowed down the norfloxacin (NOR) degradation. OTC inhibited the TN retention and promoted the HS accumulation, both NOR and EM microbial agent inhibited the TN retention and HS accumulation, while EM microbial agent showed an antagonistic effect on TN immobilization with antibiotics and reduced the impacts of antibiotics on HS. Obvious bacterial community successions occurred. Firmicutes were related to HS transformation, while Firmicutes, Actinobacteriota and Proteobacteria were associated with nitrogen conversion. NOR promoted the transformations of NH4+-N to NO3--N and FA to HA. The findings provided theoretical data for the recycle of antibiotic-contaminated manure and the efficient production of high-quality compost.
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Affiliation(s)
- Huaxuan Zhao
- Poultry Insititute, Chinese Academy of Agricultural Sciences, Yangzhou 225003, China
| | - Shangmin Li
- Poultry Insititute, Chinese Academy of Agricultural Sciences, Yangzhou 225003, China; College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yixiu Jiang
- Poultry Insititute, Chinese Academy of Agricultural Sciences, Yangzhou 225003, China
| | - Danpin Wang
- Poultry Insititute, Chinese Academy of Agricultural Sciences, Yangzhou 225003, China
| | - Hongzhi Wang
- Poultry Insititute, Chinese Academy of Agricultural Sciences, Yangzhou 225003, China
| | - Xinhong Dou
- Poultry Insititute, Chinese Academy of Agricultural Sciences, Yangzhou 225003, China
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13
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Patel N, Patel N, Pal S, Nathani N, Pandit R, Patel M, Patel N, Joshi C, Parekh B. Distinct gut and vaginal microbiota profile in women with recurrent implantation failure and unexplained infertility. BMC Womens Health 2022; 22:113. [PMID: 35413875 PMCID: PMC9004033 DOI: 10.1186/s12905-022-01681-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Female reproductive tract dysbiosis impacts implantation. However, whether gut dysbiosis influences implantation failure and whether it accompanies reproductive tract dysbiosis remains scantly explored. Herein, we examined the gut-vaginal microbiota axis in infertile women. METHODS We recruited 11 fertile women as the controls, and a cohort of 20 infertile women, 10 of whom had recurrent implantation failure (RIF), and another 10 had unexplained infertility (UE). Using amplicon sequencing, which employs PCR to create sequences of DNA called amplicon, we compared the diversity, structure, and composition of faecal and vaginal bacteria of the controls with that of the infertile cohort. Of note, we could only sequence 8 vaginal samples in each group (n = 24/31). RESULT Compared with the controls, α-diversity and β-diversity of the gut bacteria among the infertile groups differed significantly (p < 0.05). Taxa analysis revealed enrichment of Gram-positive bacteria in the RIF group, whereas Gram-negative bacteria were relatively abundant in the UE group. Strikingly, mucus-producing genera declined in the infertile cohort (p < 0.05). Hungatella, associated with trimethylamine N-oxide (TMAO) production, were enriched in the infertile cohort (p < 0.05). Vaginal microbiota was dominated by the genus Lactobacillus, with Lactobacillus iners AB-1 being the most abundant species across the groups. Compared with the infertile cohort, overgrowth of anaerobic bacteria, associated with vaginal dysbiosis, such as Leptotrichia and Snethia, occurred in the controls. CONCLUSION The gut microbiota had little influence on the vaginal microbiota. Gut dysbiosis and vaginal eubiosis occurred in the infertile women, whereas the opposite trend occurred in the controls.
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Affiliation(s)
- Nayna Patel
- Akanksha Hospital and Research Institute, Lambhvel Road, Lambhvel, Anand, Gujarat, 387310, India
| | - Nidhi Patel
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382011, India
| | - Sejal Pal
- Akanksha Hospital and Research Institute, Lambhvel Road, Lambhvel, Anand, Gujarat, 387310, India
| | - Neelam Nathani
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382011, India.,School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Visat - Gandhinagar Road, Chandkheda, Ahmedabad, Gujarat, 382424, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382011, India
| | - Molina Patel
- Akanksha Hospital and Research Institute, Lambhvel Road, Lambhvel, Anand, Gujarat, 387310, India
| | - Niket Patel
- Akanksha Hospital and Research Institute, Lambhvel Road, Lambhvel, Anand, Gujarat, 387310, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382011, India
| | - Bhavin Parekh
- Akanksha Hospital and Research Institute, Lambhvel Road, Lambhvel, Anand, Gujarat, 387310, India.
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14
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Nakazawa-Miklasevica M, Daneberga Z, Murmane D, Kroica J, Cupane L, Isarova D, Berga-Svitina E, Masinska M, Miklasevics E. Alterations of Gut Microbiota among Children with Autism Spectrum Disorder. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2021. [DOI: 10.3103/s0891416821050104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Liu H, Ye X, Chen S, Sun A, Duan X, Zhang Y, Zou H, Zhang Y. Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148381. [PMID: 34146805 DOI: 10.1016/j.scitotenv.2021.148381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Manures, storages for antibiotic resistance genes (ARGs), pollute soil and water as well as endanger human health. Recently, we have been searching a better solution to remove antibiotics and ARGs during aerobic composting. Here, the dynamics of chitosan addition on the profiles of 71 ARGs, bacterial communities, chlortetracycline (CTC), ofloxacin (OFX) were investigated in chicken manure composting and compared with zeolite addition. Chitosan addition effectively reduces antibiotics contents (CTC under detection limit, OFX 90.96%), amounts (18) and abundance (56.7%, 11.1% higher than zeolite addition) of ARGs and mobile genetic elements (MGEs) after 42 days composting. Network analysis indicated that a total of 27 genera strains assigned into 4 phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) were the potential hosts of ARGs. Redundancy analysis (RDA) demonstrated that bacterial community succession is the main contributor in the variation of ARGs. Overall, chitosan addition may effect bacterial composition by influencing physic-chemical properties and the concentration of antibiotics, Cu2+, Zn2+ to reduce the risk of ARG transmission. This study gives a new strategy about antibiotics and ARGs removal from composting on the basis of previous studies.
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Affiliation(s)
- Hongdou Liu
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Xuhong Ye
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Songling Chen
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Aobo Sun
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Xinying Duan
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Yanqing Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China; Institute of Agricultural Environment and Sustainable Development, Chinese Academy of Agricultural Sciences, China
| | - Hongtao Zou
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China.
| | - Yulong Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
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16
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Liu FY, Wen J, Hou J, Zhang SQ, Sun CB, Zhou LC, Yin W, Pang WL, Wang C, Ying Y, Han SS, Yan JY, Li CX, Yuan JL, Xing HJ, Yang ZS. Gastrodia remodels intestinal microflora to suppress inflammation in mice with early atherosclerosis. Int Immunopharmacol 2021; 96:107758. [PMID: 34162137 DOI: 10.1016/j.intimp.2021.107758] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Accepted: 05/01/2021] [Indexed: 10/21/2022]
Abstract
Atherosclsis is a critical actuator causing cardiac-cerebral vascular disease with a complicated pathogeneon, refered to the disorders of intestinal flora and persistent inflammation. Gastrodin (4-(hydroxymethyl) phenyl-β-D- Glucopyranoside) is the most abundant glucoside extracted from the Gastrodiaelata, which is a traditional Chinese herbal medicine for cardiac-cerebral vascular disease, yet its mechanisms remain little known. In the present study, the gastrodia extract and gastrodin attenuate the lipid deposition and foam cells on the inner membrane of the inner membrane of the thoracic aorta in the early atherosclerosis mice. Blood lipid detection tips that TC and LDL-C were reduced in peripheral blood after treatment with the gastrodia extract and gastrodin. Furthermore, unordered gut microbes are remodeled in terms of bacterial diversity and abundance at family and genus level. Also, the intestinal mucosa damage and permeability were reversed, accompaniedwith the reducing of inflammatory cytokines. Our findings revealed that the functions of gastrodia extract and gastrodin in cardiac-cerebral vascular disease involved to rescued gut microbes and anti-inflammation may be the mechanismof remission lipid accumulation.
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Affiliation(s)
- Fei-Yu Liu
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Jing Wen
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Jiong Hou
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Si-Qi Zhang
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Chun-Bin Sun
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Luo-Chuan Zhou
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Wen Yin
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Wen-Lin Pang
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Cui Wang
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yi Ying
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Si-Si Han
- PingHu Hospital Shenzhen University, Shenzhen University, Shenzhen, Guangdong, China
| | - Jin-Yuan Yan
- Central Laboratory, Kunming Medical University Second Hospital, Kunming, Yunnan, China.
| | - Chen-Xi Li
- PhD Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Jia-Li Yuan
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China; Key Laboratory of Microcosmic Syndrome Differentiation, Education Department of Yunnan, Kunming, Yunnan University of Chinese Medicine, Yunnan, China
| | - Hai-Jing Xing
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China; Key Laboratory of Microcosmic Syndrome Differentiation, Education Department of Yunnan, Kunming, Yunnan University of Chinese Medicine, Yunnan, China.
| | - Zhong-Shan Yang
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China; Key Laboratory of Microcosmic Syndrome Differentiation, Education Department of Yunnan, Kunming, Yunnan University of Chinese Medicine, Yunnan, China.
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17
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Durán C, Ciucci S, Palladini A, Ijaz UZ, Zippo AG, Sterbini FP, Masucci L, Cammarota G, Ianiro G, Spuul P, Schroeder M, Grill SW, Parsons BN, Pritchard DM, Posteraro B, Sanguinetti M, Gasbarrini G, Gasbarrini A, Cannistraci CV. Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome. Nat Commun 2021; 12:1926. [PMID: 33771992 PMCID: PMC7997970 DOI: 10.1038/s41467-021-22135-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
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Affiliation(s)
- Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum Munchen, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Umer Z Ijaz
- Department of Infrastructure and Environment University of Glasgow, School of Engineering, Glasgow, UK
| | - Antonio G Zippo
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche, Milan, Italy
| | | | - Luca Masucci
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Ianiro
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Pirjo Spuul
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Stephan W Grill
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bryony N Parsons
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - Brunella Posteraro
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany.
- Center for Complex Network Intelligence (CCNI) at Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, Beijing, China.
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18
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Cheng D, Liu Y, Shehata E, Feng Y, Lin H, Xue J, Li Z. In-feed antibiotic use changed the behaviors of oxytetracycline, sulfamerazine, and ciprofloxacin and related antibiotic resistance genes during swine manure composting. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123710. [PMID: 33254754 DOI: 10.1016/j.jhazmat.2020.123710] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 05/25/2023]
Abstract
The dynamics of oxytetracycline (OTC), sulfamerazine (SM1), ciprofloxacin (CIP) and related antibiotic resistance genes (ARGs) during swine manure composting were compared between manure collected from swine fed a diet containing these three antibiotics (TD) and manure directly spiked with these drugs (TS). The composting removal efficiency of OTC (94.9 %) and CIP (87.8 %) in the TD treatment was significantly higher than that of OTC (83.8 %, P < 0.01) and CIP (83.9 %, P < 0.05) in the TS treatment, while SM1 exhibited no significant difference (P > 0.05) between the two treatments. Composting effectively reduced the majority of ARGs in both TD and TS types of manure, especially tetracycline resistance genes (TRGs). Compared with the TS treatment, the abundance of some ARGs, such as tetG, qepA, sul1 and sul2, increased dramatically up to 309-fold in the TD treatment. The microbial composition of the composting system changed significantly during composting due to antibiotic feeding. Redundancy analysis suggested that the abundance of ARGs had a considerable impact on alterations in the physicochemical parameters (C/N, pH and temperature) and bacterial communities (Actinobacteria, Proteobacteria and Firmicutes) during the composting of swine manure.
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Affiliation(s)
- Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Yuanwang Liu
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ebrahim Shehata
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Lin
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; Scion, Christchurch, PO Box 29237, New Zealand
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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19
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Dareng EO, Ma B, Adebamowo SN, Famooto A, Ravel J, Pharoah PP, Adebamowo CA. Vaginal microbiota diversity and paucity of Lactobacillus species are associated with persistent hrHPV infection in HIV negative but not in HIV positive women. Sci Rep 2020; 10:19095. [PMID: 33154533 PMCID: PMC7644686 DOI: 10.1038/s41598-020-76003-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 10/22/2020] [Indexed: 01/22/2023] Open
Abstract
The vaginal microbiota is thought to play a role in modulating risk of high-risk human papillomavirus (hrHPV) infection. We examined the relationship between the vaginal microbiota and persistent hrHPV infection in HIV-negative and HIV-positive women. We used 16S-rRNA sequencing to characterize the vaginal microbiota of two serial samples taken six months apart from 211 Nigerian women (67%, 142/211 HIV-positive and 33%, 69/211 HIV-negative) and evaluated the association between the vaginal microbiota and persistent hrHPV infection using generalized estimating equation logistic regression models and linear discriminant analysis effect size (LEfSe) algorithm to identify phylotypic biomarkers of persistent hrHPV infection. The high diversity microbiota, Community State Type IV-B, was the most prevalent in both HIV-negative (38% at baseline, 30% at the follow-up visit) and HIV-positive (27% at baseline, 35% at the follow-up visit) women. The relationship between the vaginal microbiota and persistent hrHPV was modified by HIV status. In HIV-negative women, women with Lactobacillus dominant microbiota had lower odds (OR: 0.35, 95% CI 0.14-0.89, p = 0.03) of persistent hrHPV compared to women with Lactobacillus deficient microbiota. While among HIV-positive women, the odds of being persistently infected with hrHPV was higher in women with Lactobacillus dominant microbiota (OR: 1.25, 95% CI 0.73-2.14 p = 0.41). This difference in effect estimates by HIV was statistically significant (p = 0.02). A high diversity vaginal microbial community with paucity of Lactobacillus species was associated with persistent hrHPV infection in HIV-negative women but not in HIV-positive women.
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Affiliation(s)
- Eileen O Dareng
- Department of Primary Care and Public Health, University of Cambridge, Cambridge, UK.,Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Bing Ma
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sally N Adebamowo
- Department of Epidemiology, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.,Center for Bioethics and Research Ibadan, Ibadan, Nigeria
| | | | - Jacques Ravel
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Paul P Pharoah
- Department of Primary Care and Public Health, University of Cambridge, Cambridge, UK
| | - Clement A Adebamowo
- Institute of Human Virology Nigeria, Abuja, Nigeria. .,Department of Epidemiology, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA. .,Center for Bioethics and Research Ibadan, Ibadan, Nigeria. .,Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD, 21201, USA.
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20
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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21
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Han M, Liu G, Chen Y, Wang D, Zhang Y. Comparative Genomics Uncovers the Genetic Diversity and Characters of Veillonella atypica and Provides Insights Into Its Potential Applications. Front Microbiol 2020; 11:1219. [PMID: 32655519 PMCID: PMC7324755 DOI: 10.3389/fmicb.2020.01219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/13/2020] [Indexed: 11/18/2022] Open
Abstract
Veillonella atypica is a bacterium that is present in the gut and the oral cavity of mammals and plays diverse roles in different niches. A recent study demonstrated that Veillonella is highly associated with marathon running and approved that V. atypica gavage improves treadmill run time in mice, revealing that V. atypica has a high biotechnological potential in improving athlete performance. However, a comprehensive analysis of the genetic diversity, function traits, and genome editing method of V. atypica remains elusive. In the present study, we conducted a systemically comparative analysis of the genetic datasets of nine V. atypica strains. The pan-genome of V. atypica consisted of 2,065 homologous clusters and exhibited an open pan-genome structure. A phylogenetic analysis of V. atypica with two different categories revealed that V. atypica OK5 was the most distant from the other eight V. atypica strains. A total of 43 orthologous genes were identified as CAZyme genes and grouped into 23 CAZyme families. The CAZyme components derived from accessory clusters contributed to the differences in the ability of the nine V. atypica strains to utilize carbohydrates. An integrated analysis of the metabolic pathways of V. atypica suggested that V. atypica strains harbored vancomycin resistance and were involved in several biosynthesis pathways of secondary metabolites. The V. atypica strains harbored four main Cas proteins, namely, CAS-Type IIIA, CAS-Type IIA, CAS-Type IIC, and CAS-Type IIID. This pilot study provides an in-depth understanding of and a fundamental knowledge about the biology of V. atypica that allow the possibility to increase the biotechnological potential of this bacterium.
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Affiliation(s)
- Maozhen Han
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Gang Liu
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Yajun Chen
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Dong Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Yan Zhang
- School of Life Sciences, Hefei Normal University, Hefei, China
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22
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Gong HZ, Lang WY, Lan HN, Fan YY, Wang TP, Chu QR, Wang JH, Li D, Zheng X, Wu M. Effects of laying breeder hens dietary β-carotene, curcumin, allicin, and sodium butyrate supplementation on the jejunal microbiota and immune response of their offspring chicks. Poult Sci 2020; 99:3807-3816. [PMID: 32731966 PMCID: PMC7597918 DOI: 10.1016/j.psj.2020.03.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/06/2020] [Accepted: 03/26/2020] [Indexed: 12/17/2022] Open
Abstract
Our long-term goal is to improve chick health and reduce the use of antibiotics in the poultry industry via maternal effects. To link jejunal microbes with chicks' different immune levels and growth performance in our previous research, this study investigated jejunal microbes, jejunal inflammation, and immune responses based on a comparison between different groups. Newly hatched Hy-Line chicks were allotted into 3 groups: a chick control group (cCON), a ciprofloxacin lactate treatment group (Cipro)—the chicks of the cCON and Cipro groups were hatched from laying breeder hens given a basal diet—and a 5-wk β-carotene, curcumin, allicin, and sodium butyrate supplementation group (cCCAB), wherein chicks hatched from laying breeder hens. All groups were fed the same diet for 4 wk; the Cipro group was given ciprofloxacin lactate in drinking water continuously. At the end of the experiment, the results demonstrated that the jejunal microbes of the Cipro group showed significant changes in alpha and beta diversity, and in taxonomy at phylum and genus levels. Statistically, a total of 67 significantly enriched (P < 0.05) taxa were identified between groups by linear discriminant analysis effect size; Firmicutes was significantly enriched (P < 0.05) in the cCCAB group, 65 taxa were significantly enriched (P < 0.05) in the Cipro group, and 32 of the 65 enriched (P < 0.05) taxa were in the Proteobacteria phylum of the Cipro group. Levels of lipopolysaccharide in jejunal content, and nuclear factor kappa-B, and tumor necrosis factor-α in jejunums of the Cipro and cCCAB groups were increased (all P < 0.05) compared to those in the cCON group. There was obvious neutrophil infiltration and upregulated (all P < 0.05) IL-6 mRNA in the Cipro group jejunums compared to the cCON and cCCAB groups. The expression of PSME3 and PSME4 genes was upregulated (all P < 0.05) in the cCCAB group compared to the cCON and Cipro groups. In conclusion, ciprofloxacin lactate administration led to potential hazards in health and growth in chicks via microbial disturbances-induced jejunal inflammation, and laying breeder hens dietary supplementation with β-carotene, curcumin, allicin, and sodium butyrate could enhance jejunal immunity of their offspring via the interaction between host innate immunity selected microbial colonization and microbiota educated adaptive immunity.
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Affiliation(s)
- H Z Gong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118
| | - W Y Lang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118
| | - H N Lan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118
| | - Y Y Fan
- College of Foreign Languages, Jilin Agricultural University, Changchun, China 130118
| | - T P Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118
| | - Q R Chu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118
| | - J H Wang
- Jilin Academy of Agricultural Sciences, Changchun, China 130124
| | - D Li
- Jilin Academy of Agricultural Sciences, Changchun, China 130124
| | - X Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118; Key Laboratory of Animal Production, Product Quality and Security (Jilin Agricultural University), Ministry of Education, Changchun, China 130118.
| | - M Wu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China 130118.
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23
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Deng YD, Peng XB, Zhao RR, Ma CQ, Li JN, Yao LQ. The intestinal microbial community dissimilarity in hepatitis B virus-related liver cirrhosis patients with and without at alcohol consumption. Gut Pathog 2019; 11:58. [PMID: 31788031 PMCID: PMC6878713 DOI: 10.1186/s13099-019-0337-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023] Open
Abstract
Background Chronic hepatitis B virus (HBV) infection-reduced liver functions are associated with intestinal microbial community dissimilarity. This study aimed to investigate the microbial community dissimilarity in patients with different grades of HBV-related liver cirrhosis. Results Serum endotoxin was increased with Child–Pugh (CP) class (A, B, and C). Veillonellaceae and Lachnospiraceae families were reduced in patients compared with controls. Megamonas and Veillonella genus was reduced and increased in patients compared with controls, respectively, especially in CPB and CPC groups. Correlation analysis showed that endotoxin content was significantly correlated with alcohol consumption (95% CI 0.100, 0.493), CP class (95% CI 0.289, 0.687) and Lachnospiraceae family level (95% CI − 0.539, − 0.122). Firmicutes/Bacteroidetes ratio was correlated with the level of Lachnospiraceae family (95% CI 0.013, 0.481), Veillonellaceae family (95% CI 0.284, 0.696), Megamonas genus (95% CI 0.101, 0.518) and Veillonella genus (95% CI 0.134, 0.545). All aforementioned bacteria were independent risk or protective factors for hepatitis. Alcohol consumption changed microbial community. Conclusions Our study demonstrated that elevated Firmicutes/Bacteroidetes ratio, reduced Megamonas genus level and increased Veillonella genus level were indicators for HBV-related liver cirrhosis. Alcohol-related pathogenesis was associated with the changed microbial community.
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Affiliation(s)
- Yong-Dong Deng
- 1Department of Infection, First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou, 730000 Gansu China
| | - Xue-Bin Peng
- 1Department of Infection, First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou, 730000 Gansu China
| | - Rong-Rong Zhao
- 1Department of Infection, First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou, 730000 Gansu China
| | - Chao-Qun Ma
- 2First Clinical Medicine of Lanzhou University, Medical College of Lanzhou University, #199 Donggang West Road, Lanzhou, 730000 Gansu China
| | - Jian-Ning Li
- 1Department of Infection, First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou, 730000 Gansu China
| | - Li-Qiong Yao
- 3Department of Laboratory, First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou, 730000 Gansu China
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24
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Rands CM, Brüssow H, Zdobnov EM. Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties. Environ Microbiol 2019; 21:3989-4001. [PMID: 31314945 DOI: 10.1111/1462-2920.14746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/02/2019] [Accepted: 07/14/2019] [Indexed: 01/05/2023]
Abstract
Negativicutes are gram-negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of gram-positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram-negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co-evolved vertically with their hosts and thus resemble gram-positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales) from gram-negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu-like candidate prophage and no clear P2-like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence-related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross-order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co-evolution despite horizontal phage mobilization.
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Affiliation(s)
- Chris M Rands
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Harald Brüssow
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
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25
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Lusk BG. Thermophiles; or, the Modern Prometheus: The Importance of Extreme Microorganisms for Understanding and Applying Extracellular Electron Transfer. Front Microbiol 2019; 10:818. [PMID: 31080440 PMCID: PMC6497744 DOI: 10.3389/fmicb.2019.00818] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/01/2019] [Indexed: 11/30/2022] Open
Abstract
Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures ∼50 - 125°C and do not use molecular oxygen (O2) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteria capable of extracellular electron transfer (EET) are positioned close to the root of the Bacteria kingdom on the tree of life. On the contrary, EET in Gram-negative mesophilic bacteria is a relatively new phenomenon that is evolutionarily distinct from Gram-positive bacteria. This suggests that EET evolved separately in Gram-positive thermophiles and Gram-negative mesophiles, and that EET in these bacterial types is a result of a convergent evolutionary process leading to homoplasy. Thus, the study of dissimilatory metal reducing thermophiles provides a glimpse into some of Earth's earliest forms of respiration. This will provide new insights for understanding biogeochemistry and the development of early Earth in addition to providing unique avenues for exploration and discovery in astrobiology. Lastly, the physiological composition of Gram-positive thermophiles, coupled with the kinetic and thermodynamic consequences of surviving at elevated temperatures, makes them ideal candidates for developing new mathematical models and designing innovative next-generation biotechnologies. KEY CONCEPTS Anaerobe: organism that does not require oxygen for growth. Chemoautotroph: organism that obtains energy by oxidizing inorganic electron donors. Convergent Evolution: process in which organisms which are not closely related independently evolve similar traits due to adapting to similar ecological niches and/or environments. Dissimilatory Metal Reduction: reduction of a metal or metalloid that uses electrons from oxidized organic or inorganic electron donors. Exoelectrogen: microorganism that performs dissimilatory metal reduction via extracellular electron transfer. Extremophiles: organisms that thrive in physical or geochemical conditions that are considered detrimental to most life on Earth. Homoplasy: a character shared by a set of species that is not shared by a common ancestor Non-synonymous Substitutions (K a ): a substitution of a nucleotide that changes a codon sequence resulting in a change in the amino acid sequence of a protein. Synonymous Substitutions (K s ): a substitution of a nucleotide that may change a codon sequence, but results in no change in the amino acid sequence of a protein. Thermophiles: a specific group of extremophiles that survive and operate at temperatures ∼50-125°C.
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Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. MICROBIAL ECOLOGY 2018; 76:801-813. [PMID: 29445826 PMCID: PMC6132499 DOI: 10.1007/s00248-018-1155-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.
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Affiliation(s)
- Adriana Cabal
- Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576, Zotzenheim, Germany
| | - Se-Ran Jun
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Piroon Jenjaroenpun
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Visanu Wanchai
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Intawat Nookaew
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Thidathip Wongsurawat
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Mary J Burgess
- Division of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Atul Kothari
- Division of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576, Zotzenheim, Germany
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - David W Ussery
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA.
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27
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Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro. Sci Rep 2017; 7:14312. [PMID: 29085002 PMCID: PMC5662621 DOI: 10.1038/s41598-017-14707-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
The introduction of different nutrient and energy sources during weaning leads to significant changes in the infant gut microbiota. We used an in vitro infant digestive and gut microbiota model system to investigate the effect of four commercially available cereal products based on either wheat, sorghum, rice or oats, on the gut microbiota of six infants. Our results indicated cereal additions induced numerous changes in the gut microbiota composition. The relative abundance of bacterial families associated with fibre degradation, Bacteroidaceae, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Ruminococcaceae and Veillonellaceae increased, whilst the abundance of Enterobacteriaceae decreased with cereal additions. Corresponding changes in the production of SCFAs showed higher concentrations of acetate following all cereal additions, whilst, propionate and butyrate varied between specific cereal additions. These cereal-specific variations in the concentrations of SCFAs showed a moderate correlation with the relative abundance of potential SCFA-producing bacterial families. Overall, our results demonstrated clear shifts in the abundance of bacterial groups associated with weaning and an increase in the production of SCFAs following cereal additions.
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Lippert K, Kedenko L, Antonielli L, Kedenko I, Gemeier C, Leitner M, Kautzky-Willer A, Paulweber B, Hackl E. Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults. Benef Microbes 2017; 8:545-556. [PMID: 28701081 DOI: 10.3920/bm2016.0184] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Obesity and associated metabolic disorders have become highly prevalent diseases worldwide, and the human gut microbiota, due to its influence on host energy metabolism, has been attributed an important role therein. This pilot study explores host-microbiota relationships in men and women affected by various types of glucose metabolism disorder. Among 20 individuals aged 58 to 71 years with either normal glucose tolerance, prediabetes, or type 2 diabetes mellitus the gut bacterial communities were compared based on barcoded 454 sequencing of 16S rRNA genes amplified from stool samples. We found that specific microbiota groups were relatively enriched or reduced in different metabolic states. Further, positive or negative associations with clinical manifestations of metabolic disease suggest that these organisms indicate and possibly contribute to metabolic impairment or health. For instance, a higher prevalence of Erysipelotrichaceae and Lachnospiraceae was found associated with metabolic disorders, and the Holdemania and Blautia genera correlated with clinical indicators of an impaired lipid and glucose metabolism. The Bacteroidetes and groups therein, by contrast, displayed inverse relationships with metabolic disease parameters and were found relatively enriched in participants not diagnosed with metabolic syndrome or obesity. Further, the prevalence of specific Clostridia and Rikenellaceae members also pointed towards a healthier metabolic state. Links with diet as an intermediate factor included positive and negative associations of Lachnospiraceae with relative consumption rates of fat and carbohydrates, respectively, and positive associations of Turicibacteraceae with the consumption of protein. Identifying critical roles of major gut microbiota components in metabolic disorders has important translational implications regarding the prevention and treatment of metabolic diseases by means of preventing or reversing dysbiosis and by controlling exacerbating diet and life style factors particularly in sensitive population groups.
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Affiliation(s)
- K Lippert
- 1 AIT Austrian Institute of Technology GmbH, Bioresources Unit, 3430 Tulln a.d. Donau, Austria
| | - L Kedenko
- 2 First Department of Internal Medicine, Paracelsus Medical University/Salzburger Landeskliniken, 5020 Salzburg, Austria
| | - L Antonielli
- 1 AIT Austrian Institute of Technology GmbH, Bioresources Unit, 3430 Tulln a.d. Donau, Austria
| | - I Kedenko
- 2 First Department of Internal Medicine, Paracelsus Medical University/Salzburger Landeskliniken, 5020 Salzburg, Austria
| | - C Gemeier
- 2 First Department of Internal Medicine, Paracelsus Medical University/Salzburger Landeskliniken, 5020 Salzburg, Austria
| | - M Leitner
- 3 Department of Internal Medicine III, Division of Endocrinology and Metabolism, Unit of Gender Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - A Kautzky-Willer
- 3 Department of Internal Medicine III, Division of Endocrinology and Metabolism, Unit of Gender Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - B Paulweber
- 2 First Department of Internal Medicine, Paracelsus Medical University/Salzburger Landeskliniken, 5020 Salzburg, Austria
| | - E Hackl
- 1 AIT Austrian Institute of Technology GmbH, Bioresources Unit, 3430 Tulln a.d. Donau, Austria
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Brumm PJ, Gowda K, Robb FT, Mead DA. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol 2016; 7:1979. [PMID: 28066333 PMCID: PMC5167688 DOI: 10.3389/fmicb.2016.01979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
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Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLCFitchburg, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
| | - Krishne Gowda
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Frank T. Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of MarylandBaltimore, MD, USA
| | - David A. Mead
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Varigen Biosciences CorporationMadison, WI, USA
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Antunes LC, Poppleton D, Klingl A, Criscuolo A, Dupuy B, Brochier-Armanet C, Beloin C, Gribaldo S. Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. eLife 2016; 5. [PMID: 27580370 PMCID: PMC5007114 DOI: 10.7554/elife.14589] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022] Open
Abstract
One of the major unanswered questions in evolutionary biology is when and how the transition between diderm (two membranes) and monoderm (one membrane) cell envelopes occurred in Bacteria. The Negativicutes and the Halanaerobiales belong to the classically monoderm Firmicutes, but possess outer membranes with lipopolysaccharide (LPS-OM). Here, we show that they form two phylogenetically distinct lineages, each close to different monoderm relatives. In contrast, their core LPS biosynthesis enzymes were inherited vertically, as in the majority of bacterial phyla. Finally, annotation of key OM systems in the Halanaerobiales and the Negativicutes shows a puzzling combination of monoderm and diderm features. Together, these results support the hypothesis that the LPS-OMs of Negativicutes and Halanaerobiales are remnants of an ancient diderm cell envelope that was present in the ancestor of the Firmicutes, and that the monoderm phenotype in this phylum is a derived character that arose multiple times independently through OM loss. DOI:http://dx.doi.org/10.7554/eLife.14589.001 The cell envelope is one of the evolutionarily oldest parts of a bacterium. This structure – made up of a cell wall and either one or two cell membranes – surrounds the bacterial cell, maintaining the cell’s structure and providing an interface through which bacteria can sense their environment and communicate. Bacteria can be broadly classed based on the number of cell membranes that their envelope consists of. Bacteria that have a single cell membrane are known as “monoderm”, whereas those with two membranes are termed “diderm”. The number of membranes that bacteria have can affect how well they resist antibacterial compounds. When, how and why bacteria switched between monoderm and diderm cell envelopes are some of the major unanswered questions in evolutionary biology. The textbook example of a monoderm cell envelope can be found in bacteria called Firmicutes. This group includes some notoriously harmful bacteria such as Staphylococcus, which can cause conditions ranging from abscesses to pneumonia. However, some Firmicutes possess two cell membranes. It was unclear how these unusual diderm Firmicutes developed a second membrane, and how they are related to their monoderm relatives. Antunes, Poppleton et al. set out to answer these questions by analyzing the information contained in the thousands of bacterial genomes that have already been described. The results indicate that Firmicutes originally had diderm envelopes, and that species with monoderm envelopes arose independently several times through the loss of their outermost membrane. Future work is needed to investigate the driving forces and the precise mechanism that led most Firmicutes to lose their outer membrane. Also, further characterization of diderm Firmicutes will provide key information about the biology of these poorly understood bacteria. DOI:http://dx.doi.org/10.7554/eLife.14589.002
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Affiliation(s)
- Luisa Cs Antunes
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Daniel Poppleton
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Andreas Klingl
- Plant Development and Electron Microscopy, Department of Biology I, Biocenter LMU, Munich, Germany
| | - Alexis Criscuolo
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Département de Microbiologie, Institut Pasteur, Paris
| | | | - Christophe Beloin
- Unité de Génétique des Biofilms, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
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Tao W, Zhang XX, Zhao F, Huang K, Ma H, Wang Z, Ye L, Ren H. High Levels of Antibiotic Resistance Genes and Their Correlations with Bacterial Community and Mobile Genetic Elements in Pharmaceutical Wastewater Treatment Bioreactors. PLoS One 2016; 11:e0156854. [PMID: 27294780 PMCID: PMC4905627 DOI: 10.1371/journal.pone.0156854] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/21/2016] [Indexed: 01/24/2023] Open
Abstract
To understand the diversity and abundance of antibiotic resistance genes (ARGs) in pharmaceutical wastewater treatment bioreactors, the ARGs in sludge from two full-scale pharmaceutical wastewater treatment plants (PWWTPs) were investigated and compared with sludge samples from three sewage treatment plants (STPs) using metagenomic approach. The results showed that the ARG abundances in PWWTP sludge ranged from 54.7 to 585.0 ppm, which were higher than those in STP sludge (27.2 to 86.4 ppm). Moreover, the diversity of ARGs in PWWTP aerobic sludge (153 subtypes) was higher than that in STP aerobic sludge (118 subtypes). In addition, it was found that the profiles of ARGs in PWWTP aerobic sludge were similar to those in STP aerobic sludge but different from those in PWWTP anaerobic sludge, suggesting that dissolve oxygen (DO) could be one of the important factors affecting the profiles of ARGs. In PWWTP aerobic sludge, aminoglycoside, sulfonamide and multidrug resistance genes were frequently detected. While, tetracycline, macrolide-lincosamide-streptogramin and polypeptide resistance genes were abundantly present in PWWTP anaerobic sludge. Furthermore, we investigated the microbial community and the correlation between microbial community and ARGs in PWWTP sludge. And, significant correlations between ARG types and seven bacterial genera were found. In addition, the mobile genetic elements (MGEs) were also examined and correlations between the ARGs and MGEs in PWWTP sludge were observed. Collectively, our results suggested that the microbial community and MGEs, which could be affected by DO, might be the main factors shaping the profiles of ARGs in PWWTP sludge.
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Affiliation(s)
- Wenda Tao
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
- * E-mail: (XXZ); (LY)
| | - Fuzheng Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Zhu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
- * E-mail: (XXZ); (LY)
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
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Hartmann P, Seebauer CT, Schnabl B. Alcoholic liver disease: the gut microbiome and liver cross talk. Alcohol Clin Exp Res 2016; 39:763-75. [PMID: 25872593 DOI: 10.1111/acer.12704] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/18/2015] [Indexed: 01/18/2023]
Abstract
Alcoholic liver disease (ALD) is a leading cause of morbidity and mortality worldwide. Alcoholic fatty liver disease can progress to steatohepatitis, alcoholic hepatitis, fibrosis, and cirrhosis. Patients with alcohol abuse show quantitative and qualitative changes in the composition of the intestinal microbiome. Furthermore, patients with ALD have increased intestinal permeability and elevated systemic levels of gut-derived microbial products. Maintaining eubiosis, stabilizing the mucosal gut barrier, or preventing cellular responses to microbial products protect from experimental ALD. Therefore, intestinal dysbiosis and pathological bacterial translocation appear fundamental for the pathogenesis of ALD. This review highlights causes for intestinal dysbiosis and pathological bacterial translocation, their relationship, and consequences for ALD. We also discuss how the liver affects the intestinal microbiota.
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Affiliation(s)
- Phillipp Hartmann
- Department of Medicine, University of California, San Diego, La Jolla, California
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33
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Identification of protein secretion systems in bacterial genomes. Sci Rep 2016; 6:23080. [PMID: 26979785 PMCID: PMC4793230 DOI: 10.1038/srep23080] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/24/2016] [Indexed: 01/08/2023] Open
Abstract
Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their diversity has lagged behind due to lack of standard annotation tools. We built online and standalone computational tools to accurately predict protein secretion systems and related appendages in bacteria with LPS-containing outer membranes. They consist of models describing the systems’ components and genetic organization to be used with MacSyFinder to search for T1SS-T6SS, T9SS, flagella, Type IV pili and Tad pili. We identified ~10,000 candidate systems in bacterial genomes, where T1SS and T5SS were by far the most abundant and widespread. All these data are made available in a public database. The recently described T6SSiii and T9SS were restricted to Bacteroidetes, and T6SSii to Francisella. The T2SS, T3SS, and T4SS were frequently encoded in single-copy in one locus, whereas most T1SS were encoded in two loci. The secretion systems of diderm Firmicutes were similar to those found in other diderms. Novel systems may remain to be discovered, since some clades of environmental bacteria lacked all known protein secretion systems. Our models can be fully customized, which should facilitate the identification of novel systems.
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34
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Kunisawa T. Evolutionary relationships of completely sequenced Clostridia species and close relatives. Int J Syst Evol Microbiol 2015; 65:4276-4283. [DOI: 10.1099/ijsem.0.000638] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.
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Affiliation(s)
- Takashi Kunisawa
- Department of Applied Biological Sciences, Science University of Tokyo, Yamasaki 2641, Noda 278-8510, Japan
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35
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Rodríguez-Ruano SM, Martín-Vivaldi M, Martín-Platero AM, López-López JP, Peralta-Sánchez JM, Ruiz-Rodríguez M, Soler JJ, Valdivia E, Martínez-Bueno M. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird. PLoS One 2015; 10:e0139734. [PMID: 26445111 PMCID: PMC4596831 DOI: 10.1371/journal.pone.0139734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/15/2015] [Indexed: 12/16/2022] Open
Abstract
Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.
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Affiliation(s)
| | | | | | | | | | - Magdalena Ruiz-Rodríguez
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain
| | - Juan J Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, Granada, Spain
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Campbell C, Adeolu M, Gupta RS. Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov. Int J Syst Evol Microbiol 2015; 65:3203-3215. [PMID: 25999592 DOI: 10.1099/ijs.0.000347] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.
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Affiliation(s)
- Chantal Campbell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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37
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Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 2015; 15:141-61. [PMID: 25722247 PMCID: PMC4361730 DOI: 10.1007/s10142-015-0433-4] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/18/2022]
Abstract
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.
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Affiliation(s)
- Miriam Land
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Loren Hauser
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996 USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996 USA
| | - Se-Ran Jun
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Intawat Nookaew
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Michael R. Leuze
- Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tae-Hyuk Ahn
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tatiana Karpinets
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, 2800 Denmark
| | - Guruprased Kora
- Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Trudy Wassenaar
- Molecular Microbiology and Genomics Consultants, Tannenstr 7, 55576 Zotzenheim, Germany
| | - Suresh Poudel
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - David W. Ussery
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996 USA
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, 2800 Denmark
- Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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