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Sasso JM, Ammar RM, Tenchov R, Lemmel S, Kelber O, Grieswelle M, Zhou QA. Gut Microbiome-Brain Alliance: A Landscape View into Mental and Gastrointestinal Health and Disorders. ACS Chem Neurosci 2023; 14:1717-1763. [PMID: 37156006 DOI: 10.1021/acschemneuro.3c00127] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Gut microbiota includes a vast collection of microorganisms residing within the gastrointestinal tract. It is broadly recognized that the gut and brain are in constant bidirectional communication, of which gut microbiota and its metabolic production are a major component, and form the so-called gut microbiome-brain axis. Disturbances of microbiota homeostasis caused by imbalance in their functional composition and metabolic activities, known as dysbiosis, cause dysregulation of these pathways and trigger changes in the blood-brain barrier permeability, thereby causing pathological malfunctions, including neurological and functional gastrointestinal disorders. In turn, the brain can affect the structure and function of gut microbiota through the autonomic nervous system by regulating gut motility, intestinal transit and secretion, and gut permeability. Here, we examine data from the CAS Content Collection, the largest collection of published scientific information, and analyze the publication landscape of recent research. We review the advances in knowledge related to the human gut microbiome, its complexity and functionality, its communication with the central nervous system, and the effect of the gut microbiome-brain axis on mental and gut health. We discuss correlations between gut microbiota composition and various diseases, specifically gastrointestinal and mental disorders. We also explore gut microbiota metabolites with regard to their impact on the brain and gut function and associated diseases. Finally, we assess clinical applications of gut-microbiota-related substances and metabolites with their development pipelines. We hope this review can serve as a useful resource in understanding the current knowledge on this emerging field in an effort to further solving of the remaining challenges and fulfilling its potential.
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Affiliation(s)
- Janet M Sasso
- CAS, a division of the American Chemical Society, 2540 Olentangy River Rd, Columbus, Ohio 43202, United States
| | - Ramy M Ammar
- Bayer Consumer Health, R&D Digestive Health, Darmstadt 64295, Germany
| | - Rumiana Tenchov
- CAS, a division of the American Chemical Society, 2540 Olentangy River Rd, Columbus, Ohio 43202, United States
| | - Steven Lemmel
- CAS, a division of the American Chemical Society, 2540 Olentangy River Rd, Columbus, Ohio 43202, United States
| | - Olaf Kelber
- Bayer Consumer Health, R&D Digestive Health, Darmstadt 64295, Germany
| | - Malte Grieswelle
- Bayer Consumer Health, R&D Digestive Health, Darmstadt 64295, Germany
| | - Qiongqiong Angela Zhou
- CAS, a division of the American Chemical Society, 2540 Olentangy River Rd, Columbus, Ohio 43202, United States
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2
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Deng F, Liu J, Xie Z, Li S, Hu M, Lin D, Wang Y. nTiO 2 alleviates the toxic effects of TCPP on mussels by adjusting respiratory metabolism and gut microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158176. [PMID: 35995159 DOI: 10.1016/j.scitotenv.2022.158176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
As a good carrier of contaminants, nanotitanium dioxide (nTiO2) can absorb organic pollutants, producing toxicological effects on organisms. However, the complex effects of nTiO2 with contaminants on marine mussels are still unclear. In this study, we exposed mussels to tris (2-chloropropyl) phosphate (TCPP) 100 μg/L (T1), 0.5 mg/L nTiO2 + 100 μg/L TCPP (T2), 1.0 mg/L nTiO2 + 100 μg/L TCPP (T3) and control (0 nTiO2 + 0 μg/L TCPP) treatments, and assessed the combined effects of TCPP with nTiO2 on the thick-shelled mussel Mytilus coruscus by detecting the activities of gill pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH) and succinate dehydrogenase (SDH), also gill acetylcholine (Ach) and muscle lactic acid (LD) contents and gut microbiota after 14-d exposure. Compared with the control group, PK activity was increased significantly, but SDH, LDH activities and LD content were decreased significantly in T1, with the addition of nTiO2, there were not significantly different in T3. However, Ach content in T3 was significantly higher than the control and T1. Moreover, KEGG of the gut microbiota via 16 s rRNA sequencing showed that most pathways returned to the control level in T3. The results showed that TCPP affected the respiratory metabolism of mussels, changed the community structure of intestinal microflora in mussels, and nTiO2 alleviated the toxicity of TCPP. Our study provides new insights for ecological risk assessment of TCPP in bivalves in the complex aquatic environment and the novel role of nTiO2 in regulating the toxicity of TCPP.
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Affiliation(s)
- Fujing Deng
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jiani Liu
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Zhe Xie
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Saishuai Li
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Menghong Hu
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China.
| | - Youji Wang
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
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Kumar R, Pandit P, Kumar D, Patel Z, Pandya L, Kumar M, Joshi C, Joshi M. Landfill microbiome harbour plastic degrading genes: A metagenomic study of solid waste dumping site of Gujarat, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146184. [PMID: 33752005 DOI: 10.1016/j.scitotenv.2021.146184] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 05/21/2023]
Abstract
Globally, environmental pollution by plastic waste has become a severe ecological and social problem worldwide. The present study aimed to analyse the bacterial community structure and functional potential of the landfill site using high throughput shotgun metagenomic approach to understand plastic degrading capabilities present in the municipal solid waste (MSW) dumping site. In this study, soil, leachate and compost samples were collected from various locations (height and depth) of the Pirana landfill site in Ahmedabad city Gujarat, India. In total 30 phyla, 58 class, 125 order, 278 families, 793 genera, and 2468 species were predicted. The most dominant phyla detected were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria in the soil and compost samples. Whereas, in leachate samples, the predominant phyla belonged to Firmicutes (54.24%) followed by Actinobacteria (43.67%) and Proteobacteria (1.02%). The functional profiling revealed the presence of enzymatic groups and pathways involved in biodegradation of xenobiotics. The results also demonstrated the presence of potential genes that is associated with the biodegradation of different types of plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS). Present study extablishes the relationship between microbial community structure and rich sources of gene pool, which are actively involved in biodegradation of plastic waste in landfill sites.
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Affiliation(s)
- Raghawendra Kumar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Priti Pandit
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Labdhi Pandya
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, Gujarat 382355, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India.
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İnal N, Hazırolan G. A case of bacteremia caused by Leptotrichia trevisanii in pediatric patient with febrile neutropenia and review of literature. Acta Microbiol Immunol Hung 2021. [PMID: 34051072 DOI: 10.1556/030.2021.01358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022]
Abstract
Leptotrichia species are fastidious anaerobic, fusiform, pencil-shaped Gram-negative bacilli that reside in microbiota of humans. Leptotrichia species have increasingly been recognized as an opportunistic pathogen in humans, mainly in the immunocompromised patient. Anaerobic organisms have rarely been isolated from blood cultures of pediatric patients. In our study, we isolated Leptotrichia trevisanii from central venous catheter culture of a five-year-old male patient. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The early recognition of anaerobic bacteremia and administration of appropriate antimicrobial and play an important role preventing mortality and morbidity in children. In our study we report a rarely diagnosed case of L. trevisanii bacteremia in a pediatric patient.
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Affiliation(s)
- Neşe İnal
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gülşen Hazırolan
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Liu L, Sun F, Zhao H, Mi H, He S, Chen Y, Liu Y, Lan H, Zhang M, Wang Z. Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143383. [PMID: 33189382 DOI: 10.1016/j.scitotenv.2020.143383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
Due to the geographical circumstances, the Yangtze River Estuary (YRE) and the adjacent East China Sea are extensively influenced by both anthropogenic activities and environmental factors. To reveal the responses of microbes in surface sediment to environmental factors and their contributions to the biogeochemical cycle in this area, surface sediment and overlying water samples were collected at 21 stations from the estuary to the coastal region. Water and sediment parameters were determined, and 16S rRNA genes of microbes in sediment samples were sequenced using high throughput sequencing technology. The results indicated that ocean currents, sediment density (SD), nutrients, sulfate (SO42-), and salinity were the key factors shaping the microbial communities. Coastal microbes were affected mainly by SD, whereas anthropogenic discharge might have been responsible for a decrease in indigenous microbial diversity in the ocean. Due to the anthropogenic discharge, the most representative bacteria in the nearshore were aerobic and chemoheterotrophic bacteria, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, and polyphosphate accumulating organisms. In the offshore, anaerobic bacteria, thermophilic bacteria, halophilic bacteria, sulfate-reducing bacteria, and sulfide oxidizing bacteria were the dominant bacteria, and these were characterized by strong solidarity and cooperative properties within the malnourished environment. In summary, these results provide a new perspective for revealing the biogeochemical significance of the bacterial lineages in the YRE, as well as constructive guidance for the management of the marginal sea ecosystems in distinct regions.
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Affiliation(s)
- Lili Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Feifei Sun
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hanbin Zhao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Haosheng Mi
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siqi He
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ya Chen
- School of Environment Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hailian Lan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meng Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Zhiping Wang
- School of Environment Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Zhang Y, Gu Y, Chen Y, Huang Z, Li M, Jiang W, Chen J, Rao W, Luo S, Chen Y, Chen J, Li L, Jia Y, Liu M, Zhou F. Dingxin Recipe IV attenuates atherosclerosis by regulating lipid metabolism through LXR-α/SREBP1 pathway and modulating the gut microbiota in ApoE -/- mice fed with HFD. JOURNAL OF ETHNOPHARMACOLOGY 2021; 266:113436. [PMID: 33011372 DOI: 10.1016/j.jep.2020.113436] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Dingxin Recipe (DXR) is a traditional Chinese medicine formula that has been reported to be effective and safe treatment for cardiovascular diseases, such as arrhythmias, coronary heart disease. Dingxin Recipe IV (DXR IV) was further improved from the DXR according to the traditional use. However, the mechanism of DXR IV in atherosclerosis is unclear. AIM OF THE STUDY This study aimed to illustrate whether DXR IV improve atherosclerosis through modulating the lipid metabolism and gut microbiota in atherosclerosis mice. MATERIALS AND METHODS 40 male ApoE-/- mice were fed on HFD for 12 weeks and were then treated with DXR IV (1.8, 0.9, or 0.45 g/kg/d) for another 12 weeks. The decroation of DXR IV contains four traditional Chinese medicines: the dried rhizome of Coptis chinensis Franch. (15.09%), the root of Salvia miltiorrhiza Bunge (28.30%), the seed of Ziziphus jujuba Mill. (37.74%) and the fruiting body of Ganoderma lucidum (Leyss.ex Fr.) Karst. (18.87%). 8 male c57BL/6 mice fed a normal diet served as control group. The atherosclerotic plaque was quantified by oil-red O staining and masson trichrome staining. Mice feces were collected. The gut micobiota were detected by 16S rRNA gene sequencing and fecal metabolites were analyzed by 1H NMR spectroscopy. The effect of DXR IV on blood lipids (TG, TC, LDL-C, HDL-C) was investigated. The lipid metabolism related genes were determined by RT-qPCR and western blotting respectively. RESULTS DXR IV exerted the anti-atherosclerosis effect by inhibiting the excessive cholesterol deposition in aorta and regulating the level of TG, TC, LDL-C and HDL-C. The composition of gut microbiota was changed. Interestingly, the relative abundance of Muribaculaceae and Ruminococcaceae increased after DXR IV administration, whereas the abundance of Erysipelotrichaceae decreased, which have been beneficial to lipid metabolism. Nine potential metabolic biomarkers, including acetate, butyrate, propionate, alanine, succinate, valerate, xylose, choline, glutamate, were identified, which were related to fatty acid metabolism. Further, the pathway of fatty acid was detected by the RT-qPCR and western blotting. Compared with model group, the level of LXR-α and SREBP1 decreased significantly in DXR IV group while LXR-β, SREBP2 showed no statistical significance. It indicated that DXR IV modulated lipid metabolism by LXR-α/SREBP1 but not LXRβ and SREBP2. CONCLUSIONS DXR IV exhibits potential anti-atherosclerosis effect, which is closely related to lipid metabolism and the gut microbiota. This study may provide novel insights into the mechanism of DXR IV on atherosclerosis and a basis for promising clinical usage.
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Affiliation(s)
- Yaxin Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Yuyan Gu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Yihao Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Zhiyong Huang
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Mei Li
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China.
| | - Weihao Jiang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Jiahui Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Wenting Rao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Shangfei Luo
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yuyao Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Junqi Chen
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Lijun Li
- The Oncology Department, The 982 Hospital of PLA, Tangshan, Hebei Province, China.
| | - Yuhua Jia
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Menghua Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Fenghua Zhou
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
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7
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Galliguez T, Tsou PY, Cabrera A, Fergie J. Next-generation sequencing-based clinical metagenomics identifies Prevotella pleuritidis in a diabetic adolescent with large parapneumonic effusion and negative growth of pleural fluid culture: a case report. Br J Biomed Sci 2021; 78:101-105. [PMID: 32993476 DOI: 10.1080/09674845.2020.1827846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report a 12-year-old diabetic boy with a right-sided parapneumonic effusion and pneumonia who failed initial empirical antibiotics. Prevotella pleuritidis was identified from the pleural fluid using next-generation sequencing-based clinical metagenomics with cultures of pleural fluid and blood resulting negative. The patient responded well to intravenous meropenem followed by oral metronidazole.
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Affiliation(s)
- T Galliguez
- Department of Pediatrics, Driscoll Children's Hospital and College of Medicine, Texas A&M University , Corpus Christi, TX, USA
| | - P Y Tsou
- Department of Pediatrics, Driscoll Children's Hospital and College of Medicine, Texas A&M University , Corpus Christi, TX, USA
| | - A Cabrera
- Department of Pediatrics, Driscoll Children's Hospital and College of Medicine, Texas A&M University , Corpus Christi, TX, USA
| | - J Fergie
- Department of Pediatrics, Driscoll Children's Hospital and College of Medicine, Texas A&M University , Corpus Christi, TX, USA
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Albonico F, Barelli C, Albanese D, Manica M, Partel E, Rosso F, Ripellino S, Pindo M, Donati C, Zecconi A, Mortarino M, Hauffe HC. Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet. PLoS One 2020; 15:e0237262. [PMID: 32760129 PMCID: PMC7410245 DOI: 10.1371/journal.pone.0237262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.
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Affiliation(s)
- Francesca Albonico
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Department of Veterinary Medicine, Universiy of Milan, Milan, Italy
| | - Claudia Barelli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Mattia Manica
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Erika Partel
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Fausta Rosso
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Silvia Ripellino
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Massimo Pindo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all’ Adige (TN), Trento, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Alfonso Zecconi
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Heidi C. Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
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9
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Ma L, Xu S, Liu H, Xu T, Hu L, Zhao N, Han X, Zhang X. Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau. PeerJ 2019; 7:e7645. [PMID: 31579584 PMCID: PMC6754979 DOI: 10.7717/peerj.7645] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/08/2019] [Indexed: 12/18/2022] Open
Abstract
The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP.
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Affiliation(s)
- Li Ma
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China.,University of Chinese Academy of Science, Beijing, The People's Republic of China.,Qinghai Grassland Station, Xining, The People's Republic of China
| | - Shixiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China
| | - Hongjin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China.,University of Chinese Academy of Science, Beijing, The People's Republic of China
| | - Tianwei Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China
| | - Linyong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China
| | - Xueping Han
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China.,University of Chinese Academy of Science, Beijing, The People's Republic of China
| | - Xiaoling Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, The People's Republic of China.,University of Chinese Academy of Science, Beijing, The People's Republic of China
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10
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Hou H, Chen Z, Tian L, Sun Z. Leptotrichia trevisanii bacteremia in a woman with systemic lupus erythematosus receiving high-dose chemotherapy. BMC Infect Dis 2018; 18:661. [PMID: 30547754 PMCID: PMC6295021 DOI: 10.1186/s12879-018-3495-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/01/2018] [Indexed: 12/31/2022] Open
Abstract
Background Leptotrichia species are aerotolerant, Gram-negative fusiform bacteria. Cases of bacteremia caused by Leptotrichia trevisanii in immunocompromised patients have been rarely reported. Case presentation A 33-year-old female with systemic lupus erythematosus (SLE) was admitted to the department of rheumatology with bleeding from a mucosal ulcer. One month previously, she had visited our hospital and begun to receive methotrexate therapy, but mis-dosed for nearly 1 month at home. Methotrexate toxicity resulted in a severe oral ulcer and bone marrow suppression. On day-7 of hospital admission, she developed a fever, and Gram-negative rods (Leptotrichia trevisanii) were detected in blood cultures. She was diagnosed with methotrexate poisoning followed by L. trevisanii bacteremia. After antibiotic and detoxification therapy, she recovered from bacteremia, and the oral ulcer and bone-marrow suppression improved obviously. Conclusions This is the first reported case of Leptotrichia trevisanii bacteremia in a SLE patient who took mis-dosed an immunosuppressant and had an oral mucosal lesion.
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Affiliation(s)
- Hongyan Hou
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China
| | - Zhongju Chen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China
| | - Lei Tian
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China.
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11
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Emergent genital infection by Leptotrichia trevisanii. Infection 2018; 47:111-114. [PMID: 29980937 DOI: 10.1007/s15010-018-1175-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
We report the first case of an association between Leptotrichia trevisanii and an episode of pelvic inflammatory disease (PID) and the second case of the isolation of this infection in the cervical canal. A 45-yr-old woman was admitted to our emergency department with clinical and radiological signs and symptoms compatible with an episode of PID. She was hospitalized for intravenous antibiotic control and treatment and the subsequent surgical drainage of abscesses. Cultures were taken throughout the process, but only cultures from cervical canal exudate were positive, with the growth of L. trevisanii species. It appears important to carry out a complete microbiological screening, not limited to conventional agents, on adequate clinical samples to detect possible infectious agents that may be missed in these cases.
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12
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Yang Z, Xu X, Dai M, Wang L, Shi X, Guo R. Combination of bioaugmentation and biostimulation for remediation of paddy soil contaminated with 2,4-dichlorophenoxyacetic acid. JOURNAL OF HAZARDOUS MATERIALS 2018; 353:490-495. [PMID: 29705662 DOI: 10.1016/j.jhazmat.2018.04.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/19/2018] [Accepted: 04/21/2018] [Indexed: 06/08/2023]
Abstract
The batch and fed-batch tests were performed to evaluate the efficiency of bioaugmentation in combination with biostimulation for remediation of paddy soil contaminated with 2,4-dichlorophenoxyacetic acid (2,4-D). 2,4-D degrading enrichments were used for bioaugmentation, and effluents prepared through biological hydrogen production process were used as substrate for biostimulation. The batch tests indicated that 2,4-D degradation depended on the enrichment/substrate ratio (E/S), where E/S of 0.03 showed an excellent performance. The fed-batch tests showed that biostimulation only led to an improvement in 2,4-D degradation, while the pattern of repeated augmentation of enrichments (FRA) together with biostimulation obviously improved degradation of 2,4-D, 2-chlorophenol (2-CP) and phenol. DNA-sequencing approach showed that the FRA pattern altered the bacterial community composition, and high removal of 2,4-D, 2-CP and phenol may be attributed to the acclimation and persistence of Thauera. The findings demonstrated the importance of the FRA pattern on remediation of paddy soil contaminated with 2,4-D.
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Affiliation(s)
- Zhiman Yang
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Xiaohui Xu
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Meng Dai
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Lin Wang
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Xiaoshuang Shi
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Rongbo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China.
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13
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Ulger Toprak N, Alida C M V, Urban E, Wybo I, Justesen US, Jean-Pierre H, Morris T, Akgul O, Kulekci G, Soyletir G, Nagy E. Performance of mass spectrometric identification of clinical Prevotella species using the VITEK MS system: A prospective multi-center study. Anaerobe 2018; 54:205-209. [PMID: 29880448 DOI: 10.1016/j.anaerobe.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022]
Abstract
Prevotella species, members of the human microbiota, can cause opportunistic infections. Rapid and accurate identification of Prevotella isolates plays a critical role in successful treatment, especially since the antibiotic susceptibility profile differs between species. Studies, mostly carried out using the Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Biotyper system, showed that MALDI-TOF MS is an accurate, rapid and satisfactory method for the identification of clinically important anaerobes. In this multi-center study, we assessed the performance of the MALDI-TOF MS VITEK MS system for the identification of clinical Prevotella isolates. A total of 508 Prevotella isolates, representing 19 different species, collected from 11 European countries, Kuwait and Turkey between January 2014 and April 2016, were identified using VITEK MS (v3.0). The reliability of the identification was assessed by 16S rRNA gene sequencing. Using VITEK MS, 422 (83.1%) of the 508 isolates were identified on the species level, 459 (90.4%) on the genus level. A total of 49 (9.6%) isolates were not identified correctly. 16S rRNA gene sequencing results showed that this was partly due to the fact that several species were not represented in the database. However, some species that were represented in the database were also not identified. Five Prevotella strains were misidentified at the genus level, 2 of these strains belonged to a species not represented in the database. In general, the VITEK MS offers a reliable and rapid identification of Prevotella species, however the databases needs to be expanded.
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Affiliation(s)
- Nurver Ulger Toprak
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey.
| | - Veloo Alida C M
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, the Netherlands
| | - Edit Urban
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Helene Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Trefor Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - Oncu Akgul
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey
| | - Guven Kulekci
- Istanbul University, Faculty of Dentistry, Department of Microbiology, Istanbul, Turkey
| | - Guner Soyletir
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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14
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A multicenter survey of antimicrobial susceptibility of Prevotella species as determined by Etest methodology. Anaerobe 2018; 52:9-15. [PMID: 29860038 DOI: 10.1016/j.anaerobe.2018.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/14/2018] [Accepted: 05/16/2018] [Indexed: 11/21/2022]
Abstract
Knowledge about the antimicrobial susceptibility patterns of different Prevotella species is limited. The aim of this study was to determine the current antimicrobial susceptibility of clinical isolates of Prevotella species from different parts of Europe, Kuwait and Turkey. Activity of 12 antimicrobials against 508 Prevotella isolates, representing 19 species, were tested according to Etest methodology. EUCAST, CLSI and FDA guidelines were used for susceptibility interpretations. All Prevotella species were susceptible to piperacillin/tazobactam, imipenem, meropenem, tigecycline and metronidazole. Ampicillin/sulbactam and cefoxitin also showed good activity. Ampicillin, clindamycin, tetracycline and moxifloxacin were less active; 51.2%, 33.7%, 36.8% and 18.3% of isolates were non-susceptible, respectively. A total of 49 (9.6%) isolates were resistant to three or more antimicrobials. Prevotella bivia was the most prevalent species (n = 118) and accounted for most of the multidrug-resistant isolates. In conclusion, the level of non-susceptibility to antimicrobials, which may be used for treatment of infections involving Prevotella species, are a cause of concern. This data emphasizes the need for species level identification of clinical Prevotella isolates and periodic monitoring of their susceptibility to guide empirical treatment.
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15
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Deb-Choudhury S, Bermingham EN, Young W, Barnett MPG, Knowles SO, Harland D, Clerens S, Dyer JM. The effects of a wool hydrolysate on short-chain fatty acid production and fecal microbial composition in the domestic cat (Felis catus). Food Funct 2018; 9:4107-4121. [DOI: 10.1039/c7fo02004j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Novel animal-derived fibers are of interest for the pet food industry.
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Affiliation(s)
| | | | - Wayne Young
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Riddet Institute
- based at Massey University
| | - Matthew P. G. Barnett
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Riddet Institute
- based at Massey University
| | | | | | - Stefan Clerens
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Biomolecular Interaction Centre
- University of Canterbury
| | - Jolon M. Dyer
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Riddet Institute
- based at Massey University
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16
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Osaka T, Moriyama E, Arai S, Date Y, Yagi J, Kikuchi J, Tsuneda S. Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases. Nutrients 2017; 9:nu9121329. [PMID: 29211010 PMCID: PMC5748779 DOI: 10.3390/nu9121329] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 01/10/2023] Open
Abstract
The imbalance of gut microbiota is known to be associated with inflammatory bowel disease, but it remains unknown whether dysbiosis is a cause or consequence of chronic gut inflammation. In order to investigate the effects of gut inflammation on microbiota and metabolome, the sequential changes in gut microbiota and metabolites from the onset of colitis to the recovery in dextran sulfate sodium-induced colitic mice were characterized by using meta 16S rRNA sequencing and proton nuclear magnetic resonance (1H-NMR) analysis. Mice in the colitis progression phase showed the transient expansions of two bacterial families including Bacteroidaceae and Enterobacteriaceae and the depletion of major gut commensal bacteria belonging to the uncultured Bacteroidales family S24-7, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae. After the initiation of the recovery, commensal Lactobacillus members promptly predominated in gut while other normally abundant bacteria excluding the Erysipelotrichaceae remained diminished. Furthermore, 1H-NMR analysis revealed characteristic fluctuations in fecal levels of organic acids (lactate and succinate) associated with the disease states. In conclusion, acute intestinal inflammation is a perturbation factor of gut microbiota but alters the intestinal environments suitable for Lactobacillus members.
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Affiliation(s)
- Toshifumi Osaka
- Department of Microbiology and Immunology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Eri Moriyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Shunichi Arai
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Junji Yagi
- Department of Microbiology and Immunology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan.
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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17
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Eribe ERK, Olsen I. Leptotrichia species in human infections II. J Oral Microbiol 2017; 9:1368848. [PMID: 29081911 PMCID: PMC5646626 DOI: 10.1080/20002297.2017.1368848] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/15/2017] [Indexed: 12/19/2022] Open
Abstract
Leptotrichia species are non-motile facultative anaerobic/anaerobic bacteria that are found mostly in the oral cavity and some other parts of the human body, in animals, and even in ocean sediments. Valid species include L. buccalis, L. goodfellowii, L. hofstadii, L. honkongensis, L. shahii, L. trevisanii, and L. wadei. Some species require serum or blood for growth. All species ferment carbohydrates and produce lactic acid that may be involved with tooth decay. Acting as opportunistic pathogens, they are involved in a variety of diseases, and have been isolated from immunocompromised but also immunocompetent individuals. Mucositis, oral lesions, wounds, and abscesses may predispose to Leptotrichia septicemia. Because identification of Leptotrichia species by phenotypic features occasionally lead to misidentification, genetic techniques such as 16S rRNA gene sequencing is recommended. Early diagnosis and treatment of leptotrichia infections is important for positive outcomes. Over the last years, Leptotrichia species have been associated with several changes in taxonomy and new associations with clinical diseases. Such changes are reported in this updated review.
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Affiliation(s)
- Emenike R K Eribe
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Ingar Olsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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18
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A Birthday to Remember: ASA Founding President Sydney M. Finegold's 95th. Anaerobe 2017. [DOI: 10.1016/s1075-9964(17)30140-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Gilpin DF, Nixon KA, Bull M, McGrath SJ, Sherrard L, Rolain JM, Mahenthiralingam E, Elborn JS, Tunney MM. Evidence of persistence of Prevotella spp. in the cystic fibrosis lung. J Med Microbiol 2017; 66:825-832. [DOI: 10.1099/jmm.0.000500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- D. F. Gilpin
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - K. A. Nixon
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - M. Bull
- Cardiff School of Biosciences, Cardiff University, Wales, UK
| | - S. J. McGrath
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - L. Sherrard
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - J. M. Rolain
- Faculté de Médicine, Université de la Mediterranée, Marseilles, France
| | | | - J. S. Elborn
- School of Medicine, Dentistry and Biomedical Science, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - M. M. Tunney
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
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20
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The microbiota of marketed processed edible insects as revealed by high-throughput sequencing. Food Microbiol 2017; 62:15-22. [DOI: 10.1016/j.fm.2016.09.012] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 01/31/2023]
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21
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Eisenberg T, Fawzy A, Nicklas W, Semmler T, Ewers C. Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis. BMC Genomics 2016; 17:864. [PMID: 27809782 PMCID: PMC5093955 DOI: 10.1186/s12864-016-3206-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/25/2016] [Indexed: 11/30/2022] Open
Abstract
Background The Leptotrichiaceae are a family of fairly unnoticed bacteria containing both microbiota on mucous membranes as well as significant pathogens such as Streptobacillus moniliformis, the causative organism of streptobacillary rat bite fever. Comprehensive genomic studies in members of this family have so far not been carried out. We aimed to analyze 47 genomes from 20 different member species to illuminate phylogenetic aspects, as well as genomic and discriminatory properties. Results Our data provide a novel and reliable basis of support for previously established phylogeny from this group and give a deeper insight into characteristics of genome structure and gene functions. Full genome analyses revealed that most S. moniliformis strains under study form a heterogeneous population without any significant clustering. Analysis of infra-species variability for this highly pathogenic rat bite fever organism led to the detection of three specific variable number tandem analysis loci with high discriminatory power. Conclusions This highly useful and economical tool can be directly employed in clinical samples without laborious prior cultivation. Our and prospective case-specific data can now easily be compared by using a newly established MLVA database in order to gain a better insight into the epidemiology of this presumably under-reported zoonosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3206-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Eisenberg
- Abteilung Veterinärmedizin, Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60/H13, D-35392, Giessen, Germany.
| | - Ahmad Fawzy
- Abteilung Veterinärmedizin, Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60/H13, D-35392, Giessen, Germany.,Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza Square, 12211, Egypt.,Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392, Giessen, Germany
| | - Werner Nicklas
- Deutsches Krebsforschungszentrum, D-69120, Heidelberg, Germany
| | | | - Christa Ewers
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392, Giessen, Germany
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22
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Geographic and environmental sources of variation in bacterial community composition in a large-scale municipal landfill site in China. Appl Microbiol Biotechnol 2016; 101:761-769. [DOI: 10.1007/s00253-016-7917-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/25/2016] [Accepted: 10/04/2016] [Indexed: 01/07/2023]
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23
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Eisenberg T, Ewers C, Rau J, Akimkin V, Nicklas W. Approved and novel strategies in diagnostics of rat bite fever and other Streptobacillus infections in humans and animals. Virulence 2016; 7:630-48. [PMID: 27088660 DOI: 10.1080/21505594.2016.1177694] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rat bite fever (RBF), a worldwide occurring and most likely under-diagnosed zoonosis caused by Streptobacillus moniliformis, represents the most prominent disease of Streptobacillus infections. Recently, novel members have been described, from which a reservoir in rats and other animal species and a zoonotic potential can be assumed. Despite regularly published case reports, diagnostics of RBF continues to represent a 'diagnostic dilemma', because the mostly applied 16S rRNA sequence analysis may be uncertain for proper pathogen identification. Virtually nothing is known regarding prevalence in humans and animal reservoirs. For a realistic assessment of the pathogen's spread, epidemiology and virulence traits, future studies should focus on the genomic background of Streptobacillus. Full genome sequence analyses of a representative collection of strains might facilitate to unequivocally identify and type isolates. Prevalence studies using selective enrichment mechanisms may also enable the isolation of novel strains and candidate species of this neglected group of microorganisms.
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Affiliation(s)
| | - Christa Ewers
- b Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen , Gießen , Germany
| | - Jörg Rau
- c Chemisches und Veterinäruntersuchungsamt Stuttgart , Fellbach , Germany
| | - Valerij Akimkin
- c Chemisches und Veterinäruntersuchungsamt Stuttgart , Fellbach , Germany
| | - Werner Nicklas
- d Deutsches Krebsforschungszentrum , Heidelberg , Germany
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24
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Eisenberg T, Nicklas W, Mauder N, Rau J, Contzen M, Semmler T, Hofmann N, Aledelbi K, Ewers C. Phenotypic and Genotypic Characteristics of Members of the Genus Streptobacillus. PLoS One 2015; 10:e0134312. [PMID: 26252790 PMCID: PMC4529157 DOI: 10.1371/journal.pone.0134312] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Streptobacillus (S.) remained monotypic for almost 90 years until two new species were recently described. The type species, S. moniliformis, is one of the two etiological agents of rat bite fever, an under-diagnosed, worldwide occurring zoonosis. In a polyphasic approach field isolates and reference strains of S. moniliformis, S. hongkongensis, S. felis as well as divergent isolates were characterized by comparison of molecular data (n = 29) and from the majority also by their physiological as well as proteomic properties (n = 22). Based on growth-independent physiological profiling using VITEK2-compact, API ZYM and the Micronaut system fastidious growth-related difficulties could be overcome and streptobacilli could definitively be typed despite generally few differences. While differing in their isolation sites and dates, S. moniliformis isolates were found to possess almost identical spectra in matrix-assisted laser desorption ionization-time of flight mass spectrometry and Fourier transform infrared spectroscopy. Spectroscopic methods facilitated differentiation of S. moniliformis, S. hongkongensis and S. felis as well as one divergent isolate. Sequencing of 16S rRNA gene as well as functional genes groEL, recA and gyrB revealed only little intraspecific variability, but generally proved suitable for interspecies discrimination between all three taxa and two groups of divergent isolates.
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Affiliation(s)
- Tobias Eisenberg
- Hessian State Laboratory, Department of Veterinary Medicine, Giessen, Germany
- * E-mail:
| | | | - Norman Mauder
- Chemical and Veterinary Investigation Office (CVUA) Stuttgart, Fellbach, Germany
| | - Jörg Rau
- Chemical and Veterinary Investigation Office (CVUA) Stuttgart, Fellbach, Germany
| | - Matthias Contzen
- Chemical and Veterinary Investigation Office (CVUA) Stuttgart, Fellbach, Germany
| | | | - Nicola Hofmann
- Institute for Multiphase Processes, Leibniz University, Hannover, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
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Handal N, Bakken Jørgensen S, Smith Tunsjø H, Johnsen BO, Leegaard TM. Anaerobic blood culture isolates in a Norwegian university hospital: identification by MALDI-TOF MS vs 16S rRNA sequencing and antimicrobial susceptibility profiles. APMIS 2015; 123:749-58. [DOI: 10.1111/apm.12410] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 05/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Nina Handal
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Silje Bakken Jørgensen
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Hege Smith Tunsjø
- Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry; Unit of Gene Technology; Akershus University Hospital; Lørenskog Norway
| | - Bjørn Odd Johnsen
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Truls Michael Leegaard
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
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Micó MM, González Ó, Bacardit J, Malfeito J, Sans C. High salinity effect on bioremediation of pretreated pesticide lixiviates from greenhouses. ENVIRONMENTAL TECHNOLOGY 2015; 36:3221-3231. [PMID: 26041507 DOI: 10.1080/09593330.2015.1057541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/29/2015] [Indexed: 06/04/2023]
Abstract
Hydroponics culture greenhouses usually work in closed and semi-closed irrigation systems for nutrients and water-saving purposes. Photo-Fenton reaction has been revealed as an efficient way to depollute that kind of recycled effluents containing pesticides, even for high salinity concentrations. However, the inefficacy of organic matter chemical depletion imposes the use of a subsequent treatment. This work proposes the suitability of an integration of advanced oxidation process with a subsequent bioreactor to treat greenhouse lixiviates effluents at high or extremely high conductivity (salts concentration: up to 42 g L⁻¹). As a first step in this study, the performance of a series of sequencing batch reactors was monitored in order to check the biocompatibility of photo-Fenton pretreated effluents depending on their salinity content. In the second step, those same pretreated effluents were loaded to a biofiltration column filled with expanded clay. Finally, bacterial 16S rRNA gene sequencing was carried out to analyse microbial diversity of the biomass developed in the column. Results stated that the chemical-biological coupled system is effective for the treatment of water effluents containing pesticides. The integrated system is able to deplete more than 80% of the organic load, even under extremely high salinity.
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Affiliation(s)
- María M Micó
- a Departament d'Enginyeria Química , Universitat de Barcelona , Martí i Franquès 1, 6th floor; 08028 Barcelona , Spain
- b ACCIONA Agua , S.A.U. Avda. de les Garrigues, 22; Parque de Negocios Mas Blau II; 08820 El Prat de Llobregat, Barcelona , Spain
| | - Óscar González
- a Departament d'Enginyeria Química , Universitat de Barcelona , Martí i Franquès 1, 6th floor; 08028 Barcelona , Spain
| | - Jordi Bacardit
- b ACCIONA Agua , S.A.U. Avda. de les Garrigues, 22; Parque de Negocios Mas Blau II; 08820 El Prat de Llobregat, Barcelona , Spain
| | - Jorge Malfeito
- b ACCIONA Agua , S.A.U. Avda. de les Garrigues, 22; Parque de Negocios Mas Blau II; 08820 El Prat de Llobregat, Barcelona , Spain
| | - Carme Sans
- a Departament d'Enginyeria Química , Universitat de Barcelona , Martí i Franquès 1, 6th floor; 08028 Barcelona , Spain
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Bacterial community diversity in municipal waste landfill sites. Appl Microbiol Biotechnol 2015; 99:7745-56. [DOI: 10.1007/s00253-015-6633-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/16/2015] [Accepted: 04/19/2015] [Indexed: 11/26/2022]
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Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades. Anaerobe 2014; 28:182-98. [PMID: 24969840 DOI: 10.1016/j.anaerobe.2014.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
Abstract
The members of the phylum Fusobacteria and its two families, Fusobacteriaceae and Leptotrichiaceae, are distinguished at present mainly on the basis of their branching in the 16S rRNA gene trees and analysis of the internal transcribed spacer sequences in the 16S-23S rDNA. However, no biochemical or molecular characteristics are known that are uniquely shared by all of most members of these groups of bacteria. We report here detailed phylogenetic and comparative analyses on 45 sequenced Fusobacteria genomes to examine their evolutionary relationships and to identify molecular markers that are specific for the members of this phylum. In phylogenetic trees based on 16S rRNA gene sequences or concatenated sequences for 17 conserved proteins, members of the families Fusobacteriaceae and Leptotrichiaceae formed strongly supported clades and were clearly distinguished. In these trees, the species from the genus Fusobacterium also formed a number of well-supported clades. In parallel, comparative analyses on Fusobacteria genomes have identified 44 conserved signature indels (CSIs) in proteins involved in a broad range of functions that are either specific for the phylum Fusobacteria or a number of distinct subclades within this phylum. Seven of these CSIs in important proteins are uniquely present in the protein homologs of all sequenced Fusobacteria and they provide potential molecular markers for this phylum. Six and three other CSIs in other protein sequences are specific for members of the families Fusobacteriaceae and Leptotrichiaceae, respectively, and they provide novel molecular means for distinguishing members of these two families. Fourteen additional CSIs in different proteins, which are specific for either members of the genera Fusobacterium or Leptotrichia, or a number of other well-supported clades of Fusobacteria at multiple phylogenetic levels, provide molecular markers for these groups and information regarding the evolutionary relationships among the members of this phylum. Lastly, the present work has also identified 14 CSIs in divergent proteins that are specific for three specific subclades of Fusobacterium species, which are also indicated to be distinct by phylogenetic analyses. The members of these three Fusobacterium subclades also differ significantly from each other in their whole genome average nucleotide identities values, suggesting that they are possible candidates for recognition as different genera. The molecular markers reported here provide novel means for the identification of members of the phylum Fusobacteria and for their classification.
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29
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Wagener K, Drillich M, Baumgardt S, Kämpfer P, Busse HJ, Ehling-Schulz M. Falsiporphyromonas endometrii gen. nov., sp. nov., isolated from the post-partum bovine uterus, and emended description of the genus Porphyromonas Shah and Collins 1988. Int J Syst Evol Microbiol 2014; 64:642-649. [DOI: 10.1099/ijs.0.057307-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two black-pigmented, anaerobic bacterial strains, designated LMM 40T and LMM 41, were isolated from the bovine post-partum endometrium of two Holstein cows. The 16S rRNA gene sequences of the two strains were identical and showed the highest similarity to the 16S rRNA gene sequence of the type strain of
Porphyromonas crevioricanis
(90.2 %) but only 85.1 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus
Porphyromonas
,
Porphyromonas asaccharolytica
. The major fatty acid profiles of the two strains were similar to those of species of the genus
Porphyromonas
, containing iso-C15 : 0 as the major component and moderate amounts of anteiso-C15 : 0, iso-C13 : 0, C15 : 0 and C16 : 0. Hydroxylated fatty acids, such as iso-C14 : 0 3-OH, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, were also detected. The quinone profiles were dominated by the menaquinones MK-8 and MK-9, while spermidine was the major polyamine. The polar lipid profiles contained major amounts of phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and two unidentified lipids and minor amounts of phosphatidylglycerol, an unidentified aminolipid, a second unidentified aminophospholipid and an unidentified glycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C contents of LMM 40T and LMM 41 were 40.7 and 41.3 mol%, respectively. Based on a polyphasic approach, including phylogenetic analysis, physiological and biochemical tests as well as metabolic fingerprinting, it is proposed that the two strains are members of a novel genus and species, for which the name Falsiporphyromonas endometrii gen. nov., sp. nov. is proposed. The type strain of Falsiporphyromonas endometrii is LMM 40T ( = DSM 27210T = CCUG 64267T). An emended description of the genus
Porphyromonas
is also presented.
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Affiliation(s)
- K. Wagener
- Abteilung für Bestandsbetreuung bei Wiederkäuern, Klinik für Wiederkäuer, Veterinärmedizinische Universität, A-1210 Wien, Austria
- Abteilung für Funktionelle Mikrobiologie, IBMH, Department für Pathobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - M. Drillich
- Abteilung für Bestandsbetreuung bei Wiederkäuern, Klinik für Wiederkäuer, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - S. Baumgardt
- Abteilung für Klinische Mikrobiologie und Infektionsmedizin, IBMH, Department für Pathobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, D-35392 Giessen, Germany
| | - H.-J. Busse
- Abteilung für Klinische Mikrobiologie und Infektionsmedizin, IBMH, Department für Pathobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - M. Ehling-Schulz
- Abteilung für Funktionelle Mikrobiologie, IBMH, Department für Pathobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
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Newly cultured bacteria with broad diversity isolated from eight-week continuous culture enrichments of cow feces on complex polysaccharides. Appl Environ Microbiol 2013; 80:574-85. [PMID: 24212576 DOI: 10.1128/aem.03016-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
One of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented: Firmicutes (51.9%), Bacteroidetes (30.9%), Proteobacteria (11.1%), Actinobacteria (3.5%), Synergistetes (1.5%), and Fusobacteria (1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, B. ovatus, and B. xylanisolvens and members of the Porphyromonadaceae family. Many of the Firmicutes and Bacteroidetes isolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.
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31
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Varin KJ, Lin NH, Cohen Y. Biofouling and cleaning effectiveness of surface nanostructured reverse osmosis membranes. J Memb Sci 2013. [DOI: 10.1016/j.memsci.2013.06.064] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Amissah-Arthur KN, Farooq TA, Dhillon N, Cunliffe IA, Bansal A. Rare case of post-cataract-surgery Prevotella endophthalmitis diagnosed by polymerase chain reaction DNA sequencing. J Cataract Refract Surg 2013; 39:463-6. [PMID: 23506923 DOI: 10.1016/j.jcrs.2012.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 12/26/2022]
Abstract
We report the presentation, diagnosis, and management of endophthalmitis caused by the opportunistic Prevotella species. The case was referred to us following uneventful phacoemulsification and intraocular lens implantation. Accurate identification of this rare cause of endophthalmitis was made using bacterial polymerase chain reaction DNA sequencing. Subsequent prompt modification of antibacterial therapy allowed resolution of signs and symptoms and significant visual recovery. To our knowledge, this is the first reported case of diagnosis and management of post-cataract-surgery endophthalmitis caused by the opportunistic Prevotella species.
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33
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Ziemer CJ. Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides. MICROBIAL ECOLOGY 2013; 66:448-461. [PMID: 23354293 DOI: 10.1007/s00248-013-0185-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/09/2013] [Indexed: 06/01/2023]
Abstract
One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.
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Affiliation(s)
- Cherie J Ziemer
- USDA, Agricultural Research Service, National Laboratory for Agriculture and the Environment, Ames, IA 50010, USA.
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34
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Two cases of bacteremia caused by Leptotrichia trevisanii in patients with febrile neutropenia. J Infect Chemother 2013; 19:1181-4. [PMID: 23584842 DOI: 10.1007/s10156-013-0596-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/26/2013] [Indexed: 10/27/2022]
Abstract
We present two cases of bacteremia caused by Leptotrichia trevisanii: a 12-year-old girl with recurrent myeloid leukemia of the mandible and a 66-year-old man with esophageal carcinoma. As this filamentous bacillus showed indefinite Gram staining and the identification based on biochemical enzymatic reactions was not definitive, identification required 16s rRNA analysis. For this organism, drug sensitivity testing showed susceptiblity to each β-lactam antibiotics and clindamycin, but resistance to fluoroquinolone and erythromycin. This filamentous bacillus needs careful identification and appropriate antibiotic treatment.
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35
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Hand D, Wallis C, Colyer A, Penn CW. Pyrosequencing the canine faecal microbiota: breadth and depth of biodiversity. PLoS One 2013; 8:e53115. [PMID: 23382835 PMCID: PMC3561364 DOI: 10.1371/journal.pone.0053115] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 11/27/2012] [Indexed: 02/07/2023] Open
Abstract
Mammalian intestinal microbiota remain poorly understood despite decades of interest and investigation by culture-based and other long-established methodologies. Using high-throughput sequencing technology we now report a detailed analysis of canine faecal microbiota. The study group of animals comprised eleven healthy adult miniature Schnauzer dogs of mixed sex and age, some closely related and all housed in kennel and pen accommodation on the same premises with similar feeding and exercise regimes. DNA was extracted from faecal specimens and subjected to PCR amplification of 16S rDNA, followed by sequencing of the 5′ region that included variable regions V1 and V2. Barcoded amplicons were sequenced by Roche-454 FLX high-throughput pyrosequencing. Sequences were assigned to taxa using the Ribosomal Database Project Bayesian classifier and revealed dominance of Fusobacterium and Bacteroidetes phyla. Differences between animals in the proportions of different taxa, among 10,000 reads per animal, were clear and not supportive of the concept of a “core microbiota”. Despite this variability in prominent genera, littermates were shown to have a more similar faecal microbial composition than unrelated dogs. Diversity of the microbiota was also assessed by assignment of sequence reads into operational taxonomic units (OTUs) at the level of 97% sequence identity. The OTU data were then subjected to rarefaction analysis and determination of Chao1 richness estimates. The data indicated that faecal microbiota comprised possibly as many as 500 to 1500 OTUs.
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Affiliation(s)
- Daniel Hand
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Corrin Wallis
- WALTHAM® Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
| | - Alison Colyer
- WALTHAM® Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
| | - Charles W. Penn
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
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36
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Species identification of clinical Prevotella isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 50:1415-8. [PMID: 22301022 DOI: 10.1128/jcm.06326-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) for species identification of Prevotella was evaluated and compared with 16S rRNA gene sequencing. Using a Bruker database, 62.7% of the 102 clinical isolates were identified to the species level and 73.5% to the genus level. Extension of the commercial database improved these figures to, respectively, 83.3% and 89.2%. MALDI-TOF MS identification of Prevotella is reliable but needs a more extensive database.
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37
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Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. Appl Environ Microbiol 2011; 78:511-8. [PMID: 22081579 DOI: 10.1128/aem.06035-11] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Isolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067(T) and YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related to Phascolarctobacterium faecium ACM 3679(T), with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacterium Paraprevotella xylaniphila YIT 11841(T), in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067(T). Real-time PCR analysis also revealed that YIT 12067(T)-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 10(8) cells/g feces. These results indicate that YIT 12067(T)-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067(T) and YIT 12068 suggest that these strains represent a novel species, which we have designated Phascolarctobacterium succinatutens sp. nov.
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Sakamoto M, Ohkuma M. Identification and classification of the genus Bacteroides by multilocus sequence analysis. MICROBIOLOGY-SGM 2011; 157:3388-3397. [PMID: 21948050 DOI: 10.1099/mic.0.052332-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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39
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Naushad HS, Gupta RS. Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades. Antonie van Leeuwenhoek 2011; 101:105-24. [DOI: 10.1007/s10482-011-9628-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
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40
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Alauzet C, Marchandin H, Lozniewski A. New insights into Prevotella diversity and medical microbiology. Future Microbiol 2011; 5:1695-718. [PMID: 21133690 DOI: 10.2217/fmb.10.126] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In light of recent studies based on cultivation-independent methods, it appears that the diversity of Prevotella in human microbiota is greater than was previously assumed from cultivation-based studies, and that the implication of these bacteria in several human diseases was unrecognized. While some Prevotella taxa were found during opportunistic infections, changes in Prevotella abundance and diversity were discovered during dysbiosis-associated diseases. As member of the microbiota, Prevotella may also be considered as a reservoir for resistance genes. Greater knowledge on Prevotella diversity, as well as new insights into its pathogenic potential and implication in dysbiosis are expected from the use of human microbe identification microarrays, from whole-genome sequence analyse, and from the NIH Human Microbiome Project data. New approaches, including molecular-based methods, could contribute to improve the diagnosis of Prevotella infections.
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Affiliation(s)
- Corentine Alauzet
- Laboratoire de Bactériologie, EA 4369, Faculté de Médecine, Nancy Université, Vandoeuvre-les-Nancy, France
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41
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Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, Jünemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Pühler A, Schlüter A, Goesmann A. Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One 2011; 6:e14519. [PMID: 21297863 PMCID: PMC3027613 DOI: 10.1371/journal.pone.0014519] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 12/14/2010] [Indexed: 01/06/2023] Open
Abstract
Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation.
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Affiliation(s)
- Sebastian Jaenicke
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Christina Ander
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Thomas Bekel
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Regina Bisdorf
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | | | - Karl-Heinz Gartemann
- Department of Genetechnology/Microbiology, Bielefeld University, Bielefeld, Germany
| | - Sebastian Jünemann
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Department of Periodontology, University Hospital Münster, Münster, Germany
| | | | - Lutz Krause
- Division of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Australia
| | - Felix Tille
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Martha Zakrzewski
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alexander Goesmann
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- * E-mail:
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42
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Cooreman S, Schuermans C, Van Schaeren J, Olive N, Wauters G, Verhaegen J, Jeurissen A. Bacteraemia caused by Leptotrichia trevisanii in a neutropenic patient. Anaerobe 2010; 17:1-3. [PMID: 21184838 DOI: 10.1016/j.anaerobe.2010.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 12/07/2010] [Indexed: 11/25/2022]
Abstract
We describe an episode of Leptotrichia trevisanii bacteraemia in a neutropenic hemato-oncology patient receiving chemotherapy for Refractory Anemia with Excess Blasts-2 (RAEB-2). Although Leptotrichia spp. colonize the oral cavity and genitourinary tract, serious episodes of bacteraemia might occur in immunocompromised patients, particularly in those with severe neutropenia. Therefore, microbiologists should consider the possibility of Leptotrichia spp. septicemia in patients with blood cultures positive for gram negative bacilli, when routine microbiology tests fail to reveal a correct identification of the organism.
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Affiliation(s)
- S Cooreman
- Department of Microbiology, GZA Sint-Augustinus, Wilrijk, Belgium.
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43
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Sakamoto M, Ohkuma M. Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 2010; 59:1293-1302. [DOI: 10.1099/jmm.0.020420-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The hsp60 gene sequences were determined for 121 strains of Gram-negative anaerobic rods, including the genera Bacteroides, Barnesiella, Butyricimonas, Odoribacter, Parabacteroides, Paraprevotella, Porphyromonas, Prevotella and Tannerella. The mean pairwise hsp60 gene sequence similarity (73.8–97.1 %) between species in each genus, except for the genus Tannerella that comprises one species, was significantly less than that of the 16S rRNA gene sequence (88.3–96.3 %). Only pairwise hsp60 gene sequence similarity (97.1 %) of the genus Paraprevotella was higher than that of the 16S rRNA gene sequence (93.8 %). Each genus formed a distinct clade in the phylogenetic analysis of the hsp60 gene sequence as well as the 16S rRNA gene sequence. The phylogenetic analysis indicated a higher evolutionary rate for the hsp60 gene sequence than the 16S rRNA gene sequence, especially in the genera Porphyromonas and Prevotella. This study suggests that the hsp60 gene is a useful alternative phylogenetic marker for the identification and classification of a broad range of Gram-negative anaerobic rods.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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