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Acar C, Celik SK, Ozdemirel HO, Tuncdemir BE, Alan S, Mergen H. Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer. Folia Microbiol (Praha) 2024; 69:333-345. [PMID: 37344611 DOI: 10.1007/s12223-023-01072-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.
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Affiliation(s)
- Ceren Acar
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Inonu University, Malatya, 44280, Turkey.
| | | | - H Ozgur Ozdemirel
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| | - Beril Erdem Tuncdemir
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| | - Saadet Alan
- Faculty of Medicine, Department of Medical Pathology, Inonu University, Malatya, 44000, Turkey
| | - Hatice Mergen
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
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Hunter C, Dia K, Boykins J, Perry K, Banerjee N, Cuffee J, Armstrong E, Morgan G, Banerjee HN, Banerjee A, Bhattacharya S. An investigation for phylogenetic characterization of human Pancreatic cancer microbiome by 16SrDNA Sequencing and Bioinformatics techniques. Res Sq 2024:rs.3.rs-4140368. [PMID: 38585738 PMCID: PMC10996791 DOI: 10.21203/rs.3.rs-4140368/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Pancreatic cancer is a significant public health concern, with increasing incidence rates and limited treatment options. Recent studies have highlighted the role of the human microbiome, particularly the gut microbiota, in the development and progression of this disease. Microbial dysbiosis, characterized by alterations in the composition and function of the gut microbiota, has been implicated in pancreatic carcinogenesis through mechanisms involving chronic inflammation, immune dysregulation, and metabolic disturbances. Researchers have identified specific microbial signatures associated with pancreatic cancer, offering potential biomarkers for early detection and prognostication. By leveraging advanced sequencing and bioinformatics tools, scientists have delineated differences in the gut microbiota between pancreatic cancer patients and healthy individuals, providing insights into disease pathogenesis and potential diagnostic strategies. Moreover, the microbiome holds promise as a therapeutic target in pancreatic cancer treatment. Interventions aimed at modulating the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, have demonstrated potential in enhancing the efficacy of existing cancer therapies, including chemotherapy and immunotherapy. These approaches can influence immune responses, alter tumor microenvironments, and sensitize tumors to treatment, offering new avenues for improving patient outcomes and overcoming therapeutic resistance. Overall, understanding the complex interplay between the microbiome and pancreatic cancer is crucial for advancing our knowledge of disease mechanisms and identifying innovative therapeutic strategies. Here we report phylogenetic analysis of the 16S microbial sequences of the pancreatic cancer mice microbiome and corresponding age matched healthy mice microbiome. We successfully identified differentially abundance of microbiota in the pancreatic cancer.
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Affiliation(s)
- Colby Hunter
- Elizabeth City State University campus of The University of North Carolina
| | - Khadimou Dia
- Elizabeth City State University campus of The University of North Carolina
| | - Julia Boykins
- Elizabeth City State University campus of The University of North Carolina
| | - Karrington Perry
- Elizabeth City State University campus of The University of North Carolina
| | - Narendra Banerjee
- Elizabeth City State University campus of The University of North Carolina
| | - Jazmine Cuffee
- Elizabeth City State University campus of The University of North Carolina
| | - Erik Armstrong
- Elizabeth City State University campus of The University of North Carolina
| | - Gabrielle Morgan
- Elizabeth City State University campus of The University of North Carolina
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Bugarski-Stanojević V, Đokić M, Stamenković G, Barišić Klisarić N, Stojković O, Jojić V, Savić I. A Cryptic Subterranean Mammal Species, the Lesser Blind Mole Rat ( Nannospalax leucodon syrmiensis)-Retreated but Not Extinct. Animals (Basel) 2024; 14:774. [PMID: 38473158 DOI: 10.3390/ani14050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Blind mole rats (genus Nannospalax) attract a great deal of attention because of their cancer resistance and longevity. Due to the high rate of chromosome rearrangements, 74 Nannospalax chromosomal forms have been discovered. The convergence of their external morphology complicates their taxonomy, and many cryptic species remain unrecognized. Thus, the European N. leucodon supersp. is listed in the IUCN Red List of Threatened Species with "Data Deficient" status. It is crucial for the conservation of biodiversity to clarify its taxonomy, to recognize each cryptic species, and assign to them the correct conservation status. Of the more than 20 chromosomal forms described within N. leucodon, five cryptic species occur in Serbia. The most threatened among them-N. l. syrmiensis, described and named 50 years ago in the regions of Srem, Belgrade and Mačva-has been declared extinct in the literature, which may have negative consequences for the conservation of wildlife genetic diversity. Through five years of fieldwork and comparison of 16SrRNA and MT-CYTB gene segments between old, archived teeth and recently collected material, we show that N. l. syrmiensis is not extinct. However, its habitat has been fragmented and reduced, owing primarily to anthropogenic impact. Therefore, detailed surveillance, population-structure studies, risk assessment, and appropriate conservation measures are needed.
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Affiliation(s)
- Vanja Bugarski-Stanojević
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Marko Đokić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Gorana Stamenković
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Nataša Barišić Klisarić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Oliver Stojković
- Institute of Forensic Medicine, Faculty of Medicine, University of Belgrade, 11060 Belgrade, Serbia
| | - Vida Jojić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Ivo Savić
- Institute of Zoology, Faculty of Biology, University of Belgrade, 11060 Belgrade, Serbia
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Hosseini S, Sharifi R, Habibi A. Simultaneous removal of aliphatic and aromatic crude oil hydrocarbons by Pantoea agglomerans isolated from petroleum-contaminated soil in the west of Iran. Arch Microbiol 2024; 206:98. [PMID: 38351169 DOI: 10.1007/s00203-023-03819-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024]
Abstract
Hydrocarbons are considered as one of the most common and harmful environmental pollutants affecting human health and the environment. Bioremediation as an environmentally friendly, highly efficient, and cost-effective method in remediating oil-contaminated environments has been interesting in recent decades. In this study, hydrocarbon degrader bacterial strains were isolated from the highly petroleum-contaminated soils in the Dehloran oil field in the west of Iran. Out of 37 isolates, 15 can grow on M9 agar medium that contains 1.5 g L-1 of crude oil as the sole carbon source. The morphological, biochemical, and 16SrRNA sequencing analyses were performed for the isolates. The choosing of the isolates as the hydrocarbon degrader was examined by evaluating the efficacy of their crude oil removal at a concentration of 10 g L-1 in an aqueous medium. The results showed that five isolates belonging to Pseudomonas sp., Pseudomonas oryzihabitans, Roseomonas aestuarii, Pantoea agglomerans, and Arthrobacter sp. had a hyper hydrocarbon-degrading activity and they could remove more than 85% of the total petroleum hydrocarbon (TPH) after 96 h. The highest TPH removal of about 95.75% and biodegradation rate of 0.0997 g L-1 h-1 was observed for P. agglomerans. The gas chromatography-mass spectroscopy (GC-MS) analysis was performed during the biodegradation process by P. agglomerans to detect the degradation intermediates and final products. The results confirmed the presence of intermediates such as alcohols and fatty acids in the terminal oxidation pathway of alkanes in this biodegradation process. A promising P. agglomerans NB391 strain can remove aliphatic and aromatic hydrocarbons simultaneously.
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Affiliation(s)
- Saman Hosseini
- Department of Plant Protection, Razi University, Kermanshah, Iran
| | | | - Alireza Habibi
- Faculty of Petroleum and Chemical Engineering, Razi University, Kermanshah, Iran
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Wang J, Hu Z, Xu Q, Shi Y, Cao X, Ma Y, Wang M, Zhang C, Luo X, Lin F, Li X, Duan Y, Cai H. Gut microbiome-based noninvasive diagnostic model to predict acute coronary syndromes. Front Cell Infect Microbiol 2024; 13:1305375. [PMID: 38298920 PMCID: PMC10829574 DOI: 10.3389/fcimb.2023.1305375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
Background Previous studies have shown that alterations in the gut microbiota are closely associated with Acute Coronary Syndrome (ACS) development. However, the value of gut microbiota for early diagnosis of ACS remains understudied. Methods We recruited 66 volunteers, including 29 patients with a first diagnosis of ACS and 37 healthy volunteers during the same period, collected their fecal samples, and sequenced the V4 region of the 16S rRNA gene. Functional prediction of the microbiota was performed using PICRUSt2. Subsequently, we constructed a nomogram and corresponding webpage based on microbial markers to assist in the diagnosis of ACS. The diagnostic performance and usefulness of the model were analyzed using boostrap internal validation, calibration curves, and decision curve analysis (DCA). Results Compared to that of healthy controls, the diversity and composition of microbial community of patients with ACS was markedly abnormal. Potentially pathogenic genera such as Streptococcus and Acinetobacter were significantly increased in the ACS group, whereas certain SCFA-producing genera such as Blautia and Agathobacter were depleted. In addition, in the correlation analysis with clinical indicators, the microbiota was observed to be associated with the level of inflammation and severity of coronary atherosclerosis. Finally, a diagnostic model for ACS based on gut microbiota and clinical variables was developed with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.963 (95% CI: 0.925-1) and an AUC value of 0.948 (95% CI: 0.549-0.641) for bootstrap internal validation. The calibration curves of the model show good consistency between the actual and predicted probabilities. The DCA showed that the model had a high net clinical benefit for clinical applications. Conclusion Our study is the first to characterize the composition and function of the gut microbiota in patients with ACS and healthy populations in Southwest China and demonstrates the potential effect of the microbiota as a non-invasive marker for the early diagnosis of ACS.
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Affiliation(s)
- Jincheng Wang
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhao Hu
- Department of Geriatric Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qiuyue Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Yunnan Key Laboratory of Laboratory Medicine, Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, China
| | - Yunke Shi
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xingyu Cao
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yiming Ma
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Mingqiang Wang
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chaoyue Zhang
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiang Luo
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fanru Lin
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xianbin Li
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yong Duan
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Yunnan Key Laboratory of Laboratory Medicine, Yunnan Province Clinical Research Center for Laboratory Medicine, Kunming, China
| | - Hongyan Cai
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
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Xu YS, Wang YH, Zhong W, Zhang CP, Xiong ZF, Chen R, Mao T. Fecal microbial biomarkers in older adults with autoimmune diseases. Future Microbiol 2023; 18:949-957. [PMID: 37477509 DOI: 10.2217/fmb-2022-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
Aim: To analyze the alterations in the fecal microbiota of older adults with autoimmune disease and determine the diagnostic capabilities of microbial biomarkers. Methods: The raw data of fecal samples from 444 older adults from the publicly available American Gut Project database was analyzed. Results: It was found that there were no significant differences in the microbiota richness and evenness between older adults with autoimmune disease and healthy controls. However, significant differences were observed in the microbiota composition and structure. The subject operating characteristic curve of the eight key microbiota was obtained, and the area under curve value was 70.0%. Conclusion: Older adults with autoimmune disease showed changes in intestinal microbiota composition, which can be used as microbial biomarkers.
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Affiliation(s)
- Yu-Shuang Xu
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yi-Hua Wang
- School of Mathematics, Shandong University, Jinan, China
| | - Wen Zhong
- Department of General Practice, The Third People's Hospital of Chengdu, Chengdu, China
| | - Cui-Ping Zhang
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhi-Fan Xiong
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430077, China
| | - Rui Chen
- Department of General Practice, The Third People's Hospital of Chengdu, Chengdu, China
| | - Tao Mao
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
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Motallebirad T, Mardanshah O, Safarabadi M, Ghaffari K, Orouji MA, Abedi B, Azadi D. Screening, molecular identification, population diversity, and antibiotic susceptibility pattern of Actinomycetes species isolated from meat and meat products of slaughterhouses, restaurants, and meat stores of a developing country, Iran. Front Microbiol 2023; 14:1134368. [PMID: 37520382 PMCID: PMC10373891 DOI: 10.3389/fmicb.2023.1134368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Actinomycetes can colonize surfaces of tools and equipment and can be transferred to meat and meat products during manufacture, processing, handling, and storage. Moreover, washing the meat does not eliminate the microorganisms; it only spreads them. As a result, these opportunistic pathogens can enter the human body and cause various infections. Therefore, the aim of the current study was to screen, identify, and determine the antibiotic susceptibility of Actinomycetes species from meat and meat products in the Markazi province of Iran. Methods A total of 60 meat and meat product samples, including minced meat, mutton, beef, chicken, hamburgers, and sausages, were collected from slaughterhouses, butchers, and restaurants in the Markazi province of Iran. The samples were analyzed using standard microbiological protocols for the isolation and characterization of Actinomycetes. PCR amplification of hsp65 and 16SrRNA genes and sequence analysis of 16SrRNA were used for genus and species identification. The minimum inhibitory concentrations (MICs) of antimicrobial agents were determined by the broth microdilution method and interpreted according to the CLSI guidelines. Results A total of 21 (35%) Actinomycetes isolates from 5 genera and 12 species were isolated from 60 samples. The most prevalent Actinomycetes were from the genus Mycobacterium, with six (28.6%) isolates (M. avium complex, M. terrae, M. smegmatis, and M. novocastrense), followed by the genus Rhodococcus with five (23.8%) isolates (R. equi and R. erythropolis), the genus Actinomyces with four (19.1%) isolates (A. ruminicola and A. viscosus), the genus Nocardia with four (19.1%) isolates (N. asiatica, N. seriolae, and N. niigatensis), and the genus Streptomyces with two (9.5%) isolates (S. albus). Chicken and sausage samples had the highest and lowest levels of contamination, with six and one isolates. Respectively, the results of drug susceptibility testing (DST) showed that all isolates were susceptible to Ofloxacin, Amikacin, Ciprofloxacin, and Levofloxacin, whereas all of them were resistant to Doxycycline and Rifampicin. Discussion The findings suggest that meat and meat products play an important role as a reservoir for the transmission of Actinomycetes to humans, thus causing life-threatening foodborne diseases such as gastrointestinal and cutaneous disorders. Therefore, it is essential to incorporate basic hygiene measures into the cycle of meat production to ensure food safety.
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Affiliation(s)
- Tahereh Motallebirad
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Omid Mardanshah
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehdi Safarabadi
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Kazem Ghaffari
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Mohammad Ali Orouji
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Behnam Abedi
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Davood Azadi
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
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Mahmud MM, Kabir A, Hossain MZ, Mim SJ, Yeva IJ, Khatun M, Rahman MS, Dey MM, Nazir KHMNH. First report of Aliarcobacter cryaerophilus in ready-to-cook chicken meat samples from super shops in Bangladesh. J Adv Vet Anim Res 2023; 10:113-117. [PMID: 37155535 PMCID: PMC10122937 DOI: 10.5455/javar.2023.j659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 05/10/2023] Open
Abstract
Objective This study aimed to isolate Aliarcobacter cryaerophilus in ready-to-cook poultry meat in Bangladesh. Materials and Methods Thirty drumstick samples were collected from super shops in Dhaka city (n = 10), Mymensingh city (n = 10), and Patuakhali town (n = 10). After sample processing, they were cultured in Blood agar media with Campylobacter base using a microfilter (0.42 nm). Suspected colonies were subjected to DNA extraction and PCR assay targeting 16SrRNA genes. Then, sequencing was performed for confirmation. Results Of 30 samples, 3 (10%) were positive for A. cryaerophilus. Phylogenetic analysis shows that our isolate has strong similarities with one of the isolates from China. Conclusion The presence of this organism in ready-to-cook poultry meat is a significant concern for consumers as it bears zoonotic importance.
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Affiliation(s)
- Md. Muket Mahmud
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- These two authors contributed equally
| | - Ajran Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- These two authors contributed equally
| | - Md. Zawad Hossain
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sanjida Jamal Mim
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Israt Jahan Yeva
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Minara Khatun
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Saidur Rahman
- Department of Agricultural Economics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Madan Mohan Dey
- Department of Agricultural Sciences, Texas State University, San Marcos, TX, USA
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Wang F, Zhufeng Y, Chen Z, Xu J, Cheng Y. The composition and function profile of the gut microbiota of patients with primary Sjögren's syndrome. Clin Rheumatol 2023. [PMID: 36598587 DOI: 10.1007/s10067-022-06451-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVES This healthy volunteer control-based study was conducted to explore alterations of compositions and function of gut microbiota in Chinese pSS patients. METHOD The high-throughput Illumina Miseq sequencing method, targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene, was used to compare the microbiota communities between 30 pSS patients and 30 age-matched healthy volunteers. The intestinal dysbiosis of pSS patients was evaluated and its correlation with some disease phenotypes was analyzed. Furthermore, we performed the amino acid sequence alignment analysis to illustrate the molecular mimicry patterns of new microbial peptides. RESULTS Compared with that in healthy controls, the composition and function of the gut microbiota significantly differed in pSS patients. Certain genera and species, including genera: Escherichia-Shigella, Sardovia, Veillonella, Insteinimonas, and Lactobacillales; species: Escherichia coli, Lactobacillus phage Sal3, Lactobacillus reuteri, Lactobacillus gasseri, Streptococcus lutetiensis, Streptococcus mutans, Scardovia wiggsiae, and Fusobacterrium ulcerans were found to be enriched in the feces of pSS patients, while butyrate-producing bacteria were less abundant in pSS patients. Certain genera (including Lactobacillales) and species (including Lactobacillus gasseri) were associated with disease severity and therapy resistance parameters. Autoantigen epitopes of "WPSALPT, NPARSFG, MNPARSFG, and AFGLAIGT" from aquaporin-5 were aligned perfectly with one enriched microbiota of patients with pSS, namely Escherichia coli. CONCLUSIONS The composition and function of the gut microbiota significantly differed in pSS patients compared with that in healthy controls. Our study would facilitate the possible research on the role of gut microbiota in the pathogenesis of pSS.
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Xu YS, Wang YH, Liu Y, Sun X, Xu JS, Song Y, Jiang X, Xiong ZF, Tian ZB, Zhang CP. Alteration of the faecal microbiota composition in patients with constipation: evidence of American Gut Project. Benef Microbes 2022; 13:427-436. [PMID: 36377576 DOI: 10.3920/bm2022.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is limited information is known about the composition difference of the gut microbiota in patients with constipation and healthy controls. Here, the faecal 16S rRNA fastq sequence data of microbiota from the publicly available American Gut Project (AGP) were analysed. The tendency score matching (PSM) method was used to match in a 1:1 manner to control for confounding factors age, gender, body mass index (BMI), and country. A total of 524 participants including 262 patients with constipation and 262 healthy controls were included in this analysis. The richness and evenness of the gut microbiota in the constipation group were significantly lower than those in the control group. The dominant genera in the constipation group include Escherichia_Shigella, Pseudomonas, and Citrobacter. The dominant genera in the control group include Faecalibacterium, Prevotella, Roseburia, Clostridium_XlVa, and Blautia. The abundance of three butyrate production-related pathways were significantly higher in the constipation group than in the control groups. There was no significant difference in the diversity and gut microbiota composition in patients with constipation at different ages. In conclusion, patients with constipation showed gut microbiota and butyrate metabolism dysbiosis. This dysbiosis might provide a reference for the diagnosis and clinical therapy of diseases.
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Affiliation(s)
- Y S Xu
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China P.R
| | - Y H Wang
- School of Mathematics, Shandong University, Jinan, China P.R
| | - Y Liu
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China P.R
| | - X Sun
- Department of Gastroenterology, Qilu Hospital of Shandong University (Qingdao), Qingdao, China P.R
| | - J S Xu
- Division of Nephrology, Jiaozhou Hospital of Tongji University DongFang Hospital, Jiaozhou, China P.R
| | - Y Song
- Division of Gastroenterology, Jiaozhou Hospital of Tongji University DongFang Hospital, Jiaozhou, China P.R
| | - X Jiang
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 400400 Wuhan, China P.R
| | - Z F Xiong
- Division of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 400400 Wuhan, China P.R
| | - Z B Tian
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China P.R
| | - C P Zhang
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China P.R
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Zong Y, Hao K, Lu G, Li Y, Huang D. Characteristics of the colony structure of A 2O processes under different ultraviolet conditions in plateau areas. Environ Sci Pollut Res Int 2022; 29:67941-67952. [PMID: 35524846 DOI: 10.1007/s11356-022-19579-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
In this text, a laboratory-scale A2O was performed in Linzhi City at a 3000-m altitude. During the test operation, the UV irradiation was carried out in oxic tank for 0, 5, 10, 30, and 180 min. The 16SrRNA gene sequencing was performed on the activated sludge in anaerobic, anoxic, and oxic tanks, and the colony structure characteristics of phyla, genera, and species classification levels in the sludge were analyzed. There were significant differences in the numbers of genera and species (p ≤ 0.05). The community richness, uniformity, diversity, and other indicators differed to some degree compared with those of other regions. The analysis of composition of bacterial colonies revealed different levels. The significance test of the difference between the groups, the significance of the dominant species, and the mechanism of UV was analyzed. A CCA diagram was used to verify that UV is an important factor in the colony structure composition, and the correlation heatmap diagram was used to analyze the microorganisms that are significantly related to UV. A sample hierarchical cluster analysis showed that the time of UV exposure can be divided into two categories, and the effects of UV exposure increase sequentially as the time of exposure increases. A comprehensive analysis found that the enhancing and inhibitory effects of UV affect the composition of the colony structure in the sample, and the time of irradiation will affect the enhancing or inhibitory effect, that is, the colony structure from the samples that were irradiated for different amounts of time differs greatly.
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Affiliation(s)
- Yongchen Zong
- Res. Institute of Tibet Plateau Ecology, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China
- Water Conservancy Project & Civil Engineering College, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China
| | - Kaiyue Hao
- Water Conservancy Project & Civil Engineering College, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China
| | - Guanghua Lu
- Res. Institute of Tibet Plateau Ecology, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China.
- Water Conservancy Project & Civil Engineering College, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China.
| | - Yuanwei Li
- Water Conservancy Project & Civil Engineering College, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China
| | - Decai Huang
- Water Conservancy Project & Civil Engineering College, Tibet Agriculture & Animal, Husbandry University, Linzhi, 860000, China
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12
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Liu H, Luo L, Jiang G, Li G, Zhu C, Meng W, Zhang J, Jiao Q, Du P, Li X, Fahad S, Jie X, Liu S. Sulfur enhances cadmium bioaccumulation in Cichorium intybus by altering soil properties, heavy metal availability and microbial community in contaminated alkaline soil. Sci Total Environ 2022; 837:155879. [PMID: 35568178 DOI: 10.1016/j.scitotenv.2022.155879] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/25/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) contamination seriously threatens the soil health and food safety. Combination of amendment and accumulator plant is a green and effective technique to improve phytoremediation of Cd-contaminated alkaline soil. In this study, a potting experiment was conducted to investigate the effect of sulfur on Cd phytoextraction by Cichorium intybus (chicory). Soil chemical and microbial properties were determined to reveal the mechanism of sulfur-assisting Cd phytoremediation by chicory. Soil pH decreased from 7.77 to the lowest 7.30 with sulfur addition (0.6, 0.9 and 1.2 g kg-1, LS, MS and HS treatment); Electric conductivity, sulfate anion and available cadmium concentration increased gradually with increasing sulfur doses. Cd concentration of shoot and root significantly increased from 1.47 to 4.43 mg kg-1, 6.15 to 20.16 mg kg-1 by sulfur treatment relative to CK, which were attributed to increased available Cd concentration induced by decreased pH. Sulfur treatments significantly increased the Cd bioconcentration factor by 64.1%, 118.6%, 201.0% for shoot, 76.3%, 145.6% and 227.7% for root under LS, MS and HS relative to CK treatment, respectively (P < 0.05). However, only MS treatment significantly improved the Cd removal efficiency by 82.9% in comparison of CK treatment (P < 0.05). Microbial community diversity measured by 16SrRNA showed that Thiobacillus and Actinobacteria were the key and dominant strains of soil microbial communities after sulfur addition, which played a pivotal role in the process of sulfur oxidation involved in decrease of soil pH and the transformation of Cd forms. Correlation analysis and path analysis by structural equation model indicated that soil sulfate anion and Thiobacillus directly affected Cd removal efficiency by chicory in Cd-contaminated alkaline soil. This suggests that combination of sulfur and chicory may provide a way to promote Cd bioaccumulation for phytoremediation of Cd-contaminated alkaline soil.
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Affiliation(s)
- Haitao Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Lan Luo
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Guiying Jiang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China.
| | - Gezi Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Changwei Zhu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Weiwei Meng
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingjing Zhang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiujuan Jiao
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengqiang Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, China; Department of Agronomy, Faculty of Agricultural Sciences, The University of Haripur, Haripur 22620, Pakistan
| | - Xiaolei Jie
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Shiliang Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China.
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Xu Y, Wang Y, Xu J, Song Y, Liu B, Xiong Z. Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder. Microbiol Spectr 2022;:e0033122. [PMID: 35762814 DOI: 10.1128/spectrum.00331-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Cumulative studies have utilized high-throughput sequencing of the 16SrRNA gene to characterize the composition and structure of the microbiota in autism spectrum disorder (ASD). However, they do not always obtain consistent results; thus, conducting cross-study comparisons is necessary. This study sought to analyze the alteration of fecal microbiota and the diagnostic capabilities of gut microbiota biomarkers in individuals with ASD using the existing 16SrRNA microbial data and explore heterogeneity among studies. The raw sequence and metadata from 10 studies, including 1,019 samples, were reanalyzed. Results showed no significant difference in alpha diversity of fecal microbiota between ASD and the control group. However, a significant difference in the composition structure of fecal microbiota was observed. Given the large differences in sample selection and technical differences, the separation of fecal microbiota between ASD and controls was not observed. Subgroup analysis was performed on the basis of different country of origin, hypervariable regions, and sequencing platforms, and the dominant genera in ASD and healthy control groups were determined by linear discriminant analysis (LDA) of the effect size (LEfSe) algorithm and Wilcoxon rank-sum test. Machine learning analyses were carried out to determine the diagnostic capabilities of potential microbial biomarkers. A total of 12 genera were identified to distinguish ASD from control, and the AUC of the training set and verification set was 0.757 and 0.761, respectively. Despite cohort heterogeneity, gut microbial dysbiosis of ASD has been proven to be a widespread phenomenon. Therefore, fecal microbial markers are of great significance in diagnosing ASD diseases and possible candidates for further mechanistic study of the role of intestinal microbiota in ASD. IMPORTANCE This study provides an updated analysis to characterize the gut microbiota in ASD using 16SrRNA gene high-throughput sequencing data from 10 publicly available studies. Our analysis suggests an association between the fecal microbiota and ASD. Sample selection and technical differences between studies may interfere with the species composition analysis of the ASD group and control group. By summarizing the results of 16SrRNA gene sequencing from multiple fecal samples, we can provide evidence to support the use of microbial biomarkers to diagnose the occurrence of ASD. Our study provides a new perspective for further revealing the correlation between gut microbiota and ASD from the perspective of 16SrRNA sequencing in larger samples.
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Chen J, Zang Y, Yang Z, Qu T, Sun T, Liang S, Zhu M, Wang Y, Tang X. Composition and Functional Diversity of Epiphytic Bacterial and Fungal Communities on Marine Macrophytes in an Intertidal Zone. Front Microbiol 2022; 13:839465. [PMID: 35369473 PMCID: PMC8972133 DOI: 10.3389/fmicb.2022.839465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Marine macrophytes (seagrasses and macroalgae) and their epiphytic microorganisms play an important role in the ecological and biochemical processes of coastal oceans. However, simultaneous comparative studies on the biodiversity and functions of epiphytic bacteria and fungi associated with marine macrophytes have not been conducted. In this study, high-throughput sequencing technology was used to describe the epiphytic bacterial and fungal communities of 11 common macroalgae and 2 seagrasses from an intertidal zone of northern China and compare them with seawater communities. The results showed that Proteobacteria and Bacteroidota were the dominant bacterial phyla in marine macrophytes, whereas Ascomycota, Chytridiomycota, and Basidiomycota were the dominant fungal phyla. The alpha diversity of the bacterial and fungal communities in seagrasses was the highest of all macrophyte samples. This may have been related to their ability to recruit microorganisms from multiple sources. Host phylogeny may influence bacterial community structure, and geographical differences may influence fungal community structure. The FAPROTAX data indicated that C metabolic microbes were enriched in marine macrophytes, while the FUNGuild data indicated that undefined saprotroph, which participated in organic matter degradation, were also enriched in marine macrophytes. These findings provide a theoretical basis regarding the epiphytic microorganisms of macrophytes and may offer new insights to support the improved ecological restoration of seagrass and macroalgae beds.
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Affiliation(s)
- Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tongfei Qu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shuo Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Wyer S, Townsend DM, Ye Z, Kourtidis A, Choo YM, de Barros ALB, Donia MS, Hamann MT. Recent advances and limitations in the application of kahalalides for the control of cancer. Biomed Pharmacother 2022; 148:112676. [PMID: 35149387 DOI: 10.1016/j.biopha.2022.112676] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 11/24/2022] Open
Abstract
Since the discovery of the kahalalide family of marine depsipeptides in 1993, considerable work has been done to develop these compounds as new and biologically distinct anti-cancer agents. Clinical trials and laboratory research have yielded a wealth of data that indicates tolerance of kahalalides in healthy cells and selective activity against diseased cells. Currently, two molecules have attracted the greates level of attention, kahalalide F (KF) and isokahalalide F (isoKF, Irvalec, PM 02734, elisidepsin). Both compounds were originally isolated from the sarcoglossan mollusk Elysia rufescens but due to distinct structural characteristics it has been hypothesized and recently shown that the ultimate origin of the molecules is microbial. The search for their true source has been a subject of considerable research in the anticipation of finding new analogs and a culturable expression system that can produce sufficient material through fermentation to be industrially relevant.
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Ezeanya-Bakpa CC, Agbakoba NR, Enweani-Nwokelo IB, Oguejiofor CB. Phylogeny-based identification of Mycoplasma genitalium in a Nigerian population of apparently healthy sexually active female students. Pan Afr Med J 2022; 41:71. [PMID: 35382058 PMCID: PMC8956837 DOI: 10.11604/pamj.2022.41.71.19631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/15/2021] [Indexed: 11/11/2022] Open
Abstract
Introduction Mycoplasma genitalium is an emerging sexually transmitted pathogen. Sexually transmitted infection (STI) is still a burden for Nigerian women because it is asymptomatic. The lack of detection of M. genitalium in apparently healthy sexually active females in Nigeria is due to non-application of high throughput molecular approach. We conducted a study to identify M. genitalium in apparently healthy Nigerian female students using a phylogenetic approach. Methods one hundred endocervical swab specimens were collected from a student population of sexually active females aged 15 - 39 years. The 16SrRNA gene V1-V3 region of M. genitalium were amplified directly from the specimens before sequencing. Maximum Likelihood (ML) phylogenetic analysis was carried out to determine genetic relatedness. Results the prevalence of M. genitalium infection was 1% among students. The majority (59%) of them were between 20 - 24 years, with a mean age of 26.2 ± 2.66 years. High number of sexual partners, previous STI and irregular condom use were significantly associated (P < 0.05) with the prevalence of M. genitalium infection. There was extensive lack of knowledge (0%) about M. genitalium infection among the students. Phylogenetic analysis revealed three clades with different relatedness. Our study highlighted that 16SrRNA gene was a detector of M. genitalium, but it shared no phylogenetic relationship with other examined species from around the world. Conclusion despite a low prevalence of M. genitalium infection among the understudied group, its cause was not established; consequently, prevention and control measures should be based on health education in the general population in order to limit the spread of this pathogen. To our knowledge, this is the first study to identify M. genitalium among the general population of Nigeria using a phylogenetic approach.
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Affiliation(s)
- Chinyere Charity Ezeanya-Bakpa
- Department of Microbiology and Biotechnology, Caleb University, Lagos, Nigeria,,Corresponding author: Chinyere Charity Ezeanya-Bakpa, Department of Microbiology and Biotechnology, Caleb University, Lagos, Nigeria.
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Nisa S, Shoukat M, Bibi Y, Al Ayoubi S, Shah W, Masood S, Sabir M, Asma Bano S, Qayyum A. Therapeutic prospects of endophytic Bacillus species from Berberis lycium against oxidative stress and microbial pathogens. Saudi J Biol Sci 2022; 29:287-295. [PMID: 35002421 PMCID: PMC8716895 DOI: 10.1016/j.sjbs.2021.08.099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 12/13/2022] Open
Abstract
Endophytes are microorganisms residing within plant tissues. Bacterial endophytes are important sources for production of pharmaceutically important metabolites. Berberis lycium is an important medicinal plant and there exist no report regarding isolation and determination of bioactive potential of its bacterial endophytes. Therefore the present study was aimed to isolate and identify bacterial endophytes from Berberis lycium. The study resulted in isolation of 20 strains of bacterial endophytes. Based on their antibacterial activity three strains were identified as Bacillus cereus (LBL6), Bacillus thuringiensis (SBL3) and Bacillus anthracis (SBL4) on basis of 16SrRNA gene using universal primers. Crude ethyl acetate extracts of LBL6, SBL3 and SBL4 were further evaluated for antioxidant and antifungal activities. Moderate antioxidant activity (56 %) at a concentration of 1000 µg/mL was observed for LBL6 followed by 45 and 43 % activity by SBL4 and SBL3 respectively. Significant antifungal activity was observed against Aspergillus niger (60 %) and Aspergillus flavus (56 %) at concentration of 4 mg/mL of SBL3 and SBL4 respectively. GCMS analysis of extract (LBL6) exhibited presence of 12 bioactive secondary metabolites corresponding to antimicrobial, antifungal, antioxidant, antitumor and anticancer activities. In conclusion, present study highlighted the importance of Berberis lycium to host diverse bacterial endophytes of pharmaceutical importance.
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Affiliation(s)
- Sobia Nisa
- Department of Microbiology, The University of Haripur, Haripur 22620 Pakistan
| | - Mubarra Shoukat
- Department of Microbiology, The University of Haripur, Haripur 22620 Pakistan
| | - Yamin Bibi
- Department of Botany, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46300 Pakistan
| | - Samha Al Ayoubi
- Department of General Sciences, Prince Sultan University, Rafha Street, Riyadh, Kingdom of Saudi Arabia
| | - Waqas Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Saadia Masood
- Department of Statistics & Mathematics, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46300 Pakistan
| | - Maimoona Sabir
- Department of Microbiology, The University of Haripur, Haripur 22620 Pakistan
| | - Syeda Asma Bano
- Department of Microbiology, The University of Haripur, Haripur 22620 Pakistan
| | - Abdul Qayyum
- Department of Agronomy, The University of Haripur, Haripur 22620 Pakistan
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Zada S, Alam S, Ayoubi SA, Shakeela Q, Nisa S, Niaz Z, Khan I, Ahmed W, Bibi Y, Ahmed S, Qayyum A. Biological Transformation of Zearalenone by Some Bacterial Isolates Associated with Ruminant and Food Samples. Toxins (Basel) 2021; 13:712. [PMID: 34679005 DOI: 10.3390/toxins13100712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022] Open
Abstract
Zearalenone (ZEA) is a secondary metabolite produced by Fusarium spp., the filamentous fungi. Food and feed contamination with zearalenone has adverse effects on health and economy. ZEA degradation through microorganisms is providing a promising preventive measure. The current study includes isolation of 47 bacterial strains from 100 different food and rumen samples. Seventeen isolates showed maximum activity of ZEA reduction. A bacterial isolate, RS-5, reduced ZEA concentration up to 78.3% through ELISA analysis and 74.3% as determined through HPLC. Ten of the most efficient strains were further selected for comparison of their biodegradation activity in different conditions such as incubation period, and different growth media. The samples were analyzed after 24 h, 48 h, and 72 h of incubation. De Man Rogosa Sharp (MRS) broth, Tryptic soy broth, and nutrient broth were used as different carbon sources for comparison of activity through ELISA. The mean degradation % ± SD through ELISA and HPLC were 70.77% ± 3.935 and 69.11% ± 2.768, respectively. Optimum reducing activity was detected at 72 h of incubation, and MRS broth is a suitable medium. Phylogenetic analysis based on 16S rRNA gene nucleotide sequences confirmed that one of the bacterial isolate RS-5 bacterial isolates with higher mycotoxin degradation is identified as Bacillus subtilis isolated from rumen sample. B05 (FSL-8) bacterial isolate of yogurt belongs to the genus Lactobacillus with 99.66% similarity with Lactobacillus delbrukii. Similarly, three other bacterial isolates, D05, H05 and F04 (FS-17, FSL-2 and FS-20), were found to be the sub-species/strains Pseudomonas gessardii of genus Pseudomonas based on their similarity level of (99.2%, 96% and 96.88%) and positioning in the phylogenetic tree. Promising detoxification results were revealed through GC-MS analysis of RS-5 and FSL-8 activity.
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Maquia ISA, Fareleira P, Videira e. Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique. Microorganisms 2021; 9:microorganisms9081562. [PMID: 34442641 PMCID: PMC8400031 DOI: 10.3390/microorganisms9081562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022] Open
Abstract
(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.
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Affiliation(s)
- Ivete Sandra Alberto Maquia
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- TropiKMan Doctoral Program, NOVA SBE, 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, Maputo 3453, Mozambique;
| | - Paula Fareleira
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Isabel Videira e. Castro
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Ricardo Soares
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, Maputo 3453, Mozambique;
| | | | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo 3453, Mozambique; (A.C.); (N.S.R.)
| | - Cristina Máguas
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Obinna T. Ezeokoli
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein 9300, South Africa;
| | - Natasha Sofia Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo 3453, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- Correspondence: (I.M.); (A.I.R.-B.)
| | - Ana I. Ribeiro-Barros
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- Correspondence: (I.M.); (A.I.R.-B.)
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Darwish AA, Fawzy M, Osman WAL, El Ebissy EA. Clinicopathological and bacteriological studies on lamb bacterial enteritis and monitoring the oregano oil and vitamins A,D 3,E effect on its treatment. J Adv Vet Anim Res 2021; 8:291-299. [PMID: 34395600 PMCID: PMC8280979 DOI: 10.5455/javar.2021.h514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/03/2021] [Accepted: 04/09/2021] [Indexed: 11/22/2022] Open
Abstract
Objective: The objective of the study was to assess the effect of A,D3,E (I/M) and oregano oil extract 15% on some clinicopathological parameters during lamb bacterial enteritis treatment. Materials and Methods: Sixty Barki lambs, 20 apparently healthy (control group) and, 40 suffered from bacterial enteritis [enteric group (EG)], were subdivided into four treated groups (TGs): antibiotic group (AG), antibiotic + A,D3,E group (A + A,D3,E), antibiotic + oregano oil (AOG), and oregano group (OG). Fecal swabs were collected from EG then aseptically cultured, isolated, phenotypically identified, genotypically confirmed, and sequenced by PCR 16srRNA. Paper disk diffusion test was used for estimation of oregano oil extract 15% antibacterial activity. After blood sample aspiration from all animals, they were clinicopathologically and statistically analyzed. Results: Escherichia coli, followed by Salmonella species and then Klebsiella species, was the main causative agents of lamb diarrhea and were susceptible to oregano oil extract 15%. A + A,D3,E and AOG showed significant (p < 0.05) enhancement of some clinicopathological parameters more than AG or OG. Matrix metalloproteinases (MMP-2 and MMP-9) and total antioxidant capacity (TAC), yielded area under the curve, sensitivity, negative predictive value as 1, 100% and 100% respectively, were determined in both EG and TGs. Conclusion: Oregano oil extract 15% has good antibacterial properties against enteric bacteria in vitro and in vivo. The combination between antibiotic and antioxidant vitamins or oregano plant extract of 15% has a good impact on some clinicopathological alterations in lamb bacterial enteritis treatment. TAC, MMP-9, and MMP-2 may be good markers for the disease and its treatment follow-up.
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Affiliation(s)
- Asmaa Abdallah Darwish
- Department of animal and poultry health, animal and poultry division, Desert Research Center, Cairo, Egypt
| | - Marwa Fawzy
- Department of animal and poultry health, animal and poultry division, Desert Research Center, Cairo, Egypt
| | - Wafaa Abd-Latif Osman
- Department of animal and poultry health, animal and poultry division, Desert Research Center, Cairo, Egypt
| | - Eman A El Ebissy
- Department of animal and poultry health, animal and poultry division, Desert Research Center, Cairo, Egypt
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Schallenberg LA, Pearman JK, Burns CW, Wood SA. Spatial abundance and distribution of picocyanobacterial communities in two contrasting lakes revealed using environmental DNA metabarcoding. FEMS Microbiol Ecol 2021; 97:fiab075. [PMID: 34100943 DOI: 10.1093/femsec/fiab075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
Freshwater picocyanobacteria (Pcy) are important yet understudied components of lake ecosystems. Most previous studies have relied on cell abundances to assess Pcy dynamics in largely oligotrophic lakes, while little is known about spatial diversity and dynamics across different lake types. In the present study we assessed the horizontal-spatial abundance and community structure of Pcy in two contrasting (oligotrophic and hypertrophic) New Zealand lakes using epifluorescence microscopy and 16S rRNA metabarcoding. Pcy abundance and community composition differed significantly both between and within the oligotrophic and hypertrophic lakes. While spatial variability was observed in both study lakes, these differences were particularly pronounced in the oligotrophic, morphometrically complex Lake Wanaka where cell abundances were typically higher in bays than open-water sites and community structure differed significantly between sites. Community structuring appeared to be driven by localised environmental conditions, with different factors influencing each lake. These results suggest that single spot-samples are insufficient to gain an understanding of Pcy dynamics and consequently, phytoplankton dynamics in lakes.
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Affiliation(s)
- Lena A Schallenberg
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - John K Pearman
- Cawthron Institute, 98 Halifax St East, Private Bag 2, Nelson 7042, New Zealand
| | - Carolyn W Burns
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - Susanna A Wood
- Cawthron Institute, 98 Halifax St East, Private Bag 2, Nelson 7042, New Zealand
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Zhang W, Meng Y, Jing J, Wu Y, Li S. Influence of periodontal treatment on blood microbiotas: a clinical trial. PeerJ 2021; 9:e10846. [PMID: 33628640 PMCID: PMC7894104 DOI: 10.7717/peerj.10846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/05/2021] [Indexed: 01/05/2023] Open
Abstract
Objective To investigate the effects of periodontal treatment on the abundance and diversity of blood microbiota. Methods and Materials Twenty-seven periodontitis patients were randomly allocated to a control group (A) and two test groups (B1 and B2). Group A patients received full-mouth scaling and root planing (SRP), group B1 patients received subgingival glycine air polishing (GAP) right after SRP, and group B2 patients received subgingival glycine air polishing right before SRP. Peripheral blood samples were obtained at the baseline, the day after periodontal treatment, and 6 weeks after treatment and evaluated using nested polymerase chain reaction and 16SrRNA Gene Sequencing (Miseq platform). Results All participants exhibited significant improvements in the clinical parameters evaluated at the 6-week follow-up visit compared to the values at the baseline, but no significant differences were observed between the three groups. The total bacterial count was lowest in group B2. The bacterial species diversity (α-diversity) in group B1 was significantly higher (Chao-1 index, P = 0.03) and Porphyromonas and Pantoea were the dominant genera (linear discriminant analysis (LDA > 2)) in this group the day after treatment compared to the baseline. No significant difference was detected in the relative abundance and α-diversity of blood microbiota between the baseline and 6 weeks after treatment. Conclusion Local periodontal treatment merely disrupts the stability of blood microbiota in the short term. Periodontitis treatment using full-mouth SRP followed by adjunctive GAP is a promising approach to reduce the introduction of bacteria into the bloodstream during the procedure.
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Affiliation(s)
- Wenyi Zhang
- Department of Periodontology, Qingdao Stomatological Hospital Affliated to Qingdao University, Qingdao, Shandong, China
| | - Yang Meng
- Department of Prosthodontics, Qingdao Stomatological Hospital Affliated to Qingdao University, Qingdao, Shandong, China
| | - Jin Jing
- Department of Periodontology, Qingdao Stomatological Hospital Affliated to Qingdao University, Qingdao, Shandong, China
| | - Yingtao Wu
- Department of Periodontology, Qingdao Stomatological Hospital Affliated to Qingdao University, Qingdao, Shandong, China
| | - Shu Li
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
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23
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Franco-Lara L, García JA, Bernal YE, Rodríguez RA. Diversity of the 'Candidatus Phytoplasma asteris' and 'Candidatus Phytoplasma fraxini' isolates that infect urban trees in Bogotá, Colombia. Int J Syst Evol Microbiol 2021; 70:6508-6517. [PMID: 33174835 DOI: 10.1099/ijsem.0.004553] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas have been associated with a disease that affects trees of at least 11 species from different botanic families in Bogotá, Colombia. 'Candidatus Phytoplasma asteris' and 'Candidatus Phytoplasma fraxini' are the major groups of phytoplasma in the area of Bogotá. In this study, the genetic diversity within 'Ca. P. asteris' and 'Ca. P. fraxini' was studied in five urban tree species: Croton species (Euphorbiaceae), Fraxinus uhdei (Oleaceae), Magnolia grandiflora (Magnoliaceae), Populus nigra (Salicaceae) and Quercus humboldtii (Fagaceae). Analyses of the 16S rRNA gene using nested PCR, RFLP and sequencing showed that phytoplasmas of 'Ca. P. asteris' could be assigned to: subgroup 16SrI-B; a new subgroup named 16SrI-AF, with a restriction pattern similar to that of 16SrI-B; and a new subgroup named 16SrI-AG, with a restriction pattern similar to that of 16SrI-K and 16SrI-AH with a restriction pattern similar to that of 16SrI-AC. 'Ca. P. fraxini' isolates belonged to a new subgroup named 16SrVII-G, with a restriction pattern similar to that of 16SrVII-A. To complement the identification of the phytoplasma strains, we amplified nonribosomal genes such as leuS and secA. Unexpectedly, it was observed that in 16 trees in which 16S rRNA gene analysis showed the presence of 'Ca. P. fraxini' only, the leuS or secA primers amplified sequences exclusively affiliated to 'Ca. P. asteris. In those plants, sequences belonging to 'Ca. P. fraxini' leuS or secA genes were not amplified. The present work contributes to the identification of novel strains of both species in Colombia, and supports previous suggestions that phytoplasmas in South America are highly variable.
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Affiliation(s)
- Liliana Franco-Lara
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
| | - Jennifer Andrea García
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
| | - Yuly Eilen Bernal
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km2 vía Cajicá-Zipaquirá, Colombia.,Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
| | - Rubén Adolfo Rodríguez
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
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Zhou J, Cavagnaro TR, De Bei R, Nelson TM, Stephen JR, Metcalfe A, Gilliham M, Breen J, Collins C, López CMR. Wine Terroir and the Soil Bacteria: An Amplicon Sequencing-Based Assessment of the Barossa Valley and Its Sub-Regions. Front Microbiol 2021; 11:597944. [PMID: 33488543 PMCID: PMC7817890 DOI: 10.3389/fmicb.2020.597944] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/04/2020] [Indexed: 02/01/2023] Open
Abstract
A wines' terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.
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Affiliation(s)
- Jia Zhou
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Timothy R. Cavagnaro
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Roberta De Bei
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Tiffanie M. Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - John R. Stephen
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
- ARC Industrial Transformation Training Centre for Innovative Wine Production, Waite Research Institute, Adelaide, SA, Australia
| | - James Breen
- Bioinformatics Hub, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Cassandra Collins
- School of Agriculture Food & Wine, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
- ARC Industrial Transformation Training Centre for Innovative Wine Production, Waite Research Institute, Adelaide, SA, Australia
| | - Carlos M. Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
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Abstract
PURPOSE To explore the characteristics of gut microbiota and its relationship between clinical manifestations in patients with type 1 narcolepsy (NT1). PATIENTS AND METHODS Scale and polysomnography were performed in 20 NT1 patients and 16 healthy controls (HC group) to evaluate the clinical characteristics of NT1. Illumina sequencing was performed on bacterial 16S ribosomal RNA gene using V3-V4 regions to compare the fecal microbiota in all subjects. Associations between clinical characteristics and gut microbiota were analyzed using partial correlation analysis. RESULTS Compared with the HC group, the NT1 group had a significantly higher ESS score, longer total sleep time, increased wakefulness, decreased sleep efficiency, disturbance of sleep structure, shorter mean sleep latency, and increased sleep-onset REM periods (all P < 0.05). No differences in alpha and beta diversity were observed between the two groups. In contrast, there were significant differences at the level of class, order, family, and genus (all P < 0.05). LEfSe analysis showed that the relative abundance of Klebsiella in the NT1 group was higher than that in the HC group (P < 0.05), while the relative abundance of Blautia, Barnesiellaceae, Barnesiella, Phocea, Lactococcus, Coriobacteriia, Coriobacteriales, Ruminiclostridium_5, and Bilophila were lower (all P < 0.05). Partial correlation analysis revealed that partial differential bacteria in the NT1 group were correlated with total sleep time, sleep efficiency, stage 1 sleep, arousal index, and sleep latency (all P < 0.05). CONCLUSION Our data revealed differences in intestinal flora structure between NT1 patients and the normal population, thus providing a theoretical basis for future microecological therapy for narcolepsy. However, future larger sample size studies and different study designs are needed to further clarify the possible pathogenesis and potential causality of intestinal flora in NT1 patients and explore the new treatment strategies.
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Affiliation(s)
- Ruirui Zhang
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Henan University, Zhengzhou, Henan, People's Republic of China
| | - Shanjun Gao
- Microbiome Laboratory, Henan Provincial People's Hospital, Zhengzhou, Henan, People's Republic of China
| | - Shenghui Wang
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Jiewen Zhang
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Henan University, Zhengzhou, Henan, People's Republic of China.,Department of Neurology, Henan Provincial People's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yingying Bai
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Shuang He
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Pan Zhao
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Hongju Zhang
- Department of Neurology, Henan Provincial People's Hospital Affiliated to Henan University, Zhengzhou, Henan, People's Republic of China.,Department of Neurology, Henan Provincial People's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, People's Republic of China
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Ye M, Sun J, Chen Y, Ren Q, Li Z, Zhao Y, Pan Y, Xue H. Oatmeal induced gut microbiota alteration and its relationship with improved lipid profiles: a secondary analysis of a randomized clinical trial. Nutr Metab (Lond) 2020; 17:85. [PMID: 33042205 PMCID: PMC7542720 DOI: 10.1186/s12986-020-00505-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background In vitro and animal experiments reported a microbiota-regulating ability of oatmeal, however, related in vivo evidences remained limited. Thus, we conducted this study aiming to investigate the oatmeal-induced alteration of gut microbiota and its potential relationship with the improvements of lipid profiles. Methods and study design Data of anthropometric measurements and biochemical parameters were extracted from a randomized, controlled clinical trial, in which 62 hypercholesterolemic men and women (18-65 years old) were provided with either treatment of 80 g/day oatmeal or 80 g/day refined white rice for 45 days. Fasting blood samples and fecal samples were collected both at baseline and endpoint of the study for lipid profiling and microbiota 16S rRNA amplicon sequencing, respectively. Results Totally 28 participants (56 fecal samples) qualified with the new criteria and were thus included in this secondary analysis. The results of microbiota analysis showed that no significant difference was observed in the alteration of its overall α or β diversity between two groups throughout the study. Nor did any notable between-group difference was found in the relative abundance changes of microorganism at different taxonomies. However, results from linear discriminant analysis effect size in the oatmeal group indicated a significant positive response of Firmicutes phylum following oatmeal consumption. Further Procrustes analysis suggested a concordance trend between microorganism alteration and alleviation of hypercholesterolemia phenotypes throughout the study (P = 0.05). The results of within-group comparison from Spearman's correlation in the oatmeal group demonstrated a significant association between the enrichment of Blautia genus and the reduction of serum total cholesterol (P < 0.05), low-density lipoprotein cholesterol (P < 0.01), and apolipoprotein B (P < 0.05). Conclusions Positive response of Firmicutes phylum might be a critical characteristic of oatmeal-induced alteration of microbiota, whereas, one of the underlying cholesterol-lowering mechanism of oatmeal consumption might be its microbiota-manipulating ability, in which the enrichment of Blautia genus played a potentially significant role. Current results should be taken cautiously and more studies were needed for further verification.Trial registration: ChiCTR, ChiCTR180001864. Registered 30 September 2018, http://www.chictr.org.cn/showproj.aspx?proj=31469.
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Affiliation(s)
- Mengyao Ye
- Clinical Nutrition Center, Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Jianqin Sun
- Clinical Nutrition Center, Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Yanqiu Chen
- Clinical Nutrition Center, Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Qian Ren
- Clinical Nutrition Center, Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Zhen Li
- Clinical Nutrition Center, Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Yanfang Zhao
- Clinical Nutrition Center, Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Yiru Pan
- Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
| | - Huijun Xue
- Huadong Hospital Affiliated to Fudan University, 221 West Yan'an Road, Shanghai, 200040 People's Republic of China
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Hemmati C, Al-Subhi AM, Al-Housni M, Al-Sadi AM. First report of a subgroup 16SrII-D phytoplasma associated with Opuntia cylindrica fasciated disease in Oman. Plant Dis 2020; 105:485. [PMID: 32870114 DOI: 10.1094/pdis-04-20-0806-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cacti are evergreen perennial succulent plants that are used as ornamental and hedge plants. The fruits and leaves are also used as forage in some areas (Dewir, 2016). Cactus species are susceptible to several pathogens, including phytoplasma. In March 2020, three cactus plants (Opuntia cylindrica) out of ten (30% incidence) exhibited phytoplasma symptoms, including stunted growth, fasciation in stems and cladodes, color changes of the tips of cladodes to purple, and having clusters of highly proliferating cladodes. The plants were located in the Botanic Garden at Sultan Qaboos University, Muscat, Oman (N:23º59'14"; E:58º16'34"). PCR assays were carried out on the DNA samples extracted from young cladodes of three each of symptomatic and asymptomatic plants using phytoplasma-universal 16S rRNA primers, P1/P7 in direct PCR followed by R16F2n/R16R2, P4/P7 in the nested PCR. Distilled water (DW) and Alfalfa witches' broom phytoplasma (AlfWB) were used as negative and positive controls in each assay, respectively. In addition, amplification of the partial translocase protein A (secA) gene in the symptomatic cactus samples was done using SecA-II-F1/SecA-II-R1 (targeting 2140 bp) followed by SecA-II-F1/SecAR4 (targeting 1510 bp) (Al-Subhi et al., 2018). All the symptomatic plants and the positive control were positive for both genes (16S and secA), but no amplification was observed from the asymptomatic samples and DW. Sequence analysis and similarity searches against BLASTn revealed that the phytoplasma 16S rRNA (MT327813) shared 100% sequence identity with that of 'Candidatus Phytoplasma aurantifolia' isolate CB04 (MT555412) from India. The secA gene sequence (MT331815) analysis showed 100% identity with Cicer arietinum phyllody (KX358585). The associated phytoplasma was designated as cactus fasciated phytoplasma (CFP). Phylogenetic trees based on CFP 16Sr rRNA,secA genes, and a combined phylogenetic tree showed clustering of the CFP with the 16SrII-D subgroup phytoplasmas. The association of the aster yellows and peanut witches'-broom phytoplasma groups with other cactus species has already been reported from Lebanon, Mexico, China, Italy and Egypt (Dewir, 2016). The 16SrII phytoplasma in association with O. cylindrica showing fasciated stem has been reported from Egypt (Omar et al., 2014). A series of diverse plant species in association with 16SrII-D phytoplasma has been reported from Oman (Al-Subhi et al., 2018). However, this is the first report of a cactus phytoplasma disease in Oman belonging to the 16SrII-D subgroup phytoplasmas. Some fasciated cactus species are attractive and therefore cultivated as new ornamental plants and transported around the world, which may pose a new threat to other economically important crops.
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Affiliation(s)
- Chamran Hemmati
- Hormozgan University, 185136, Iran, Bandarabas, Iran (the Islamic Republic of), 123;
| | - Ali Masoud Al-Subhi
- College of Agricultural and Marines Sciences, SQU, Crop Sciences, Biotechnology Lab Suppervisor, Al-SEEb, Al- Khod 123, Muscut, Oman, P.O. Box-34;
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Maquia IS, Fareleira P, Videira e Castro I, Brito DRA, Soares R, Chaúque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI. Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion. Microorganisms 2020; 8:E1291. [PMID: 32846974 PMCID: PMC7563409 DOI: 10.3390/microorganisms8091291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023] Open
Abstract
(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
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Affiliation(s)
- Ivete Sandra Maquia
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
- TropiKMan Doctoral Program, Nova School of Business & Economics (Nova SBE), 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Isabel Videira e Castro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Ricardo Soares
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - M. Manuela Ferreira-Pinto
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Erica Lumini
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Andrea Berruti
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Natasha S. Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
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Legrand TPRA, Catalano SR, Wos-Oxley ML, Wynne JW, Weyrich LS, Oxley APA. Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota. Anim Microbiome 2020; 2:26. [PMID: 33499964 DOI: 10.1186/s42523-020-00046-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. RESULTS Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. CONCLUSION As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.
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Lu WW, Fu TX, Wang Q, Chen YL, Li TY, Wu GL. The effect of total glucoside of paeony on gut microbiota in NOD mice with Sjögren's syndrome based on high-throughput sequencing of 16SrRNA gene. Chin Med 2020; 15:61. [PMID: 32536964 PMCID: PMC7291443 DOI: 10.1186/s13020-020-00342-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/30/2020] [Indexed: 12/23/2022] Open
Abstract
Purpose To investigate the effect of total glucoside of paeony (TGP) on gut microbiota in NOD mice with Sjögren’s syndrome (SS), using high-throughput sequencing of 16SrRNA gene. Methods Twenty-four NOD mice were randomly assigned to 4 groups (n = 6 per group): sham group receiving deionized water (0.4 ml), hydroxychloroquin group receiving hydroxychloroquin (0.4 ml), TGP group receiving TGP (0.4 ml), and TGP + hydroxychloroquin group receiving 0.4 ml TGP and 0.4 ml hydroxychloroquin. Balb/c mice (n = 6) receiving 0.4 ml deionized water were used as a control group. After intragastric injection of drugs for 8 weeks, feces were collected for high-throughput sequencing of 16SrRNA gene. Results The sequencing of 16SrRNA gene resulted in 3686 OTUs, and 10 phyla and 69 genera were identified. Compared with the control group, the indices of Chao, Ace and Shannon in the other 4 groups were significantly lower (P < 0.05), and the Simpson index were significantly higher in the TGP, hydroxychloroquine, and sham groups (P < 0.05). Compared with the sham group, the indices of Chao, Ace and Shannon were significantly higher (P < 0.05), whereas the Simpson index was significantly lower (P < 0.05) in the TGP and TGP + hydroxychloroquine groups. At phylum level, Bacteroidetes was least abundant (36.1%), and Firmicutes was most abundant (56.28%) in the TGP + hydroxychloroquine group. Compared with the other 4 groups, Bacteroidetes was significantly less abundant (P < 0.05) and Firmicutes was significantly more abundant (P < 0.05) in the TGP + hydroxychloroquine group. Verrucomicrobia was most abundant (12.26%) in the hydroxychloroquine, and was significantly more abundant compared with the other 3 groups (P < 0.05). At genus level, compared with the control group, the abundance of Lactobacillus and Incertae of Phylum Firmicutes and Desulfovibrio of Phylum Proteobacteria was significantly increased, and the abundance of Bacteroides and Alloprevotella of Phylum Bacteroidetes and Pseudoflavonifractor of Phylum Firmicutes was significantly decreased in the TGP + hydroxychloroquine group (P < 0.05). Compared with the hydroxychloroquine group, the abundance of Akkermansia of Phylum Verrucomicrobia was significantly decreased in the TGP and TGP + hydroxychloroquine groups (P < 0.05). The abundance of Alistipes of Phylum Bacteroidetes and Desulfovibrio of Phylum Proteobacteria was significantly increased in the TGP + hydroxychloroquine group (P < 0.05). Conclusions TGP increases the growth of many key beneficial bacteria, inhibits the growth of dominant pathogenic bacteria, and increases the diversity and abundance of gut microorganisms, especially when combined with hydroxychloroquine. Our findings suggest that TGP may be effective to treat SS by improving the microecological structure of the gut.
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Affiliation(s)
- Wen-Wen Lu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003 China
| | - Tian-Xiao Fu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003 China
| | - Qing Wang
- Internal Medicine, Tongde Hospital of Zhejiang Provincial, Hangzhou, 310012 China
| | - Yi-Lian Chen
- Basic Medical College, Zhejiang University of Chinese Medicine, Hangzhou, 310053 China
| | - Tian-Yi Li
- Basic Medical College, Zhejiang University of Chinese Medicine, Hangzhou, 310053 China
| | - Guo-Lin Wu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003 China
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Qin SM, Bai WQ, Zhang KY, Ding XM, Bai SP, Wang JP, Peng HW, Yang YF, Chen C, Zeng QF. Different microbiomes are found in healthy breeder ducks and those with foot pad dermatitis. Poult Sci 2020; 98:6340-6348. [PMID: 31393583 PMCID: PMC8913756 DOI: 10.3382/ps/pez456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022] Open
Abstract
Foot pad dermatitis (FPD) is a serious problem of the modern poultry industry, negatively affecting birds' welfare and health status, walking and feeding activity, growth performance, carcass quality, and economic performance of meat production. The gut microbiome in poultry with FPD has not been previously investigated. Therefore, we compared the cecal microbiomes of 8 breeding ducks with FPD to 8 control ducks (breeders with apparently healthy feet) by pyrosequencing the bacterial 16S ribosomal RNA gene. The results showed a significant β-diversity (P < 0.05) of cecal microbiota presented between healthy and FPD-affected breeder ducks. The plasma endotoxins, interleukin 1β (IL-1β), IL-17, IL-6, IL-10, and tumor necrosis factor-α concentration, and the abundance of class Clostridia in FPD-affected ducks was markedly higher (P < 0.05), however, the abundance of genus Prevotella, Lactobacillus, Lachnospiraceae UCG-008, and the Firmicutes to Bacteroidetes ratio in FPD-affected ducks was significantly lower (P < 0.05) when compared to healthy ducks. These findings suggest when duck breeders are affected with FPD, ducks show an increased inflammatory response and a difference of structure and composition of the cecal microbiome.
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Affiliation(s)
- S M Qin
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - W Q Bai
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - K Y Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - X M Ding
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - S P Bai
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - J P Wang
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - H W Peng
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
| | - Y F Yang
- Tieqilishi Group Breeding Duck Co. Ltd., Mianyang 610000, Sichuan Province, China
| | - C Chen
- Tieqilishi Group Breeding Duck Co. Ltd., Mianyang 610000, Sichuan Province, China
| | - Q F Zeng
- Institute of Animal Nutrition, Sichuan Agricultural University; Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan Province, China
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Thakur K, Chownk M, Kumar V, Purohit A, Vashisht A, Kumar V, Yadav SK. Bioprospecting potential of microbial communities in solid waste landfills for novel enzymes through metagenomic approach. World J Microbiol Biotechnol 2020; 36:34. [PMID: 32088773 DOI: 10.1007/s11274-020-02812-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/13/2020] [Indexed: 01/19/2023]
Abstract
Landfills are repository for complex microbial diversity responsible for bio-degradation of solid waste. To elucidate this complexity, samples from three different landfill sites of North India (sample V: Bhalswa near Karnal byepass road, New Delhi, India; sample T: Chandigarh, India and sample S3: Una, H.P., India) were analyzed using metagenomic approach. Selected landfill sites had different geographical location, varied in waste composition, size of landfill and climate zone. For comparison, one sample from high altitude (sample J) having less human interference was taken in this study. The aim of this study was to explore microbial diversity of communities responsible for degradation of landfill. Samples were characterized by 16S rRNA gene sequencing. Data from three landfill sites showed abundance of phylum Proteobacteria while less contaminated sample from high altitude showed abundance of phylum Cholroflexi followed by phylum Proteobacteria. The most abundant genus was unknown suggesting that these landfills could be repository for various novel bacterial communities. Sample T was relatively more active in terms of microbial activity. It was relatively abundant in enzymes responsible for dioxin degradation, styrene degradation, steroid degradation, streptomycin biosynthesis, carbapenem biosynthesis, monobactam biosynthesis, furfural degradation pathways while sample J was predicted to be enriched in plant cell wall degrading enzymes. Co-occurrence analysis revealed presence of complex interaction networks between microbial assemblages responsible for bio-degradation of hydrocarbons. The data provides insights about synergetic interactions and functional interplay between bacterial communities in different landfill sites which could be further exploited to develop an effective bioremediation process.
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Azadi D, Motallebirad T, Ghaffari K, Shokri D, Rezaei F. Species Diversity, Molecular Characterization, and Antimicrobial Susceptibility of Opportunistic Actinomycetes Isolated from Immunocompromised and Healthy Patients of Markazi Province of Iran. Infect Drug Resist 2020; 13:1-10. [PMID: 32021315 PMCID: PMC6954848 DOI: 10.2147/idr.s234292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
Background Actinomycetes widely exist in nature and these species cause infections in immunocompromised and healthy patients, although they are frequently found as members of the normal microbiota of humans and animals. These subsequent infections are often misdiagnosed as malignancy and tuberculosis. Due to this issue, the present study aimed to determine the presence and diversity of actinomycetes species causing infections in Iranian patients. Materials and Methods A total of 79 clinical samples collected from five hospitals in Markazi province were analyzed for the existence of actinomycetes using standard protocols for isolation and characterization of the isolates. The conventional tests were used for preliminary identification, the PCR amplification of hsp65 gene, the specific region of the 16S rRNA, and sequence analyses of 16S rRNA were applied for the genus and species identification. MICs of the antimicrobial agent were determined by the broth microdilution method and interpreted according to the NCCLS guidelines. Results A total of 17 (21.51%) actinomycetes isolates were recovered from clinical samples. In other analyzed samples, eight (10.12%) gram-positive, 12 (15.18) gram-negative bacteria, and six (7.6) fungi isolates were recovered. The most prevalent actinomycetes species were M. fortuitum (17.64%), N. Mexicana and S. heliomycini (11.76% each), and 10 species, ie, N. farcinica, M. lehmannii, M. flavescens, Arthrobacter crystalopoetis, N. neocaledoniensis, M. phocaicum, M. abscessus, M. arupense, M. setense, and N. cyriacigeorgica made up the single isolates. Results of DST illustrated that all of the isolates were susceptible to Amikacin, Levofloxacin, Ofloxacin, and Ciprofloxacin, whereas all of them were resistant to Rifampicin and Doxycycline. Conclusion In conclusion, increasing isolation of actinomycetes found in various clinical cases merits special attention by health authorities in developing countries. In health centers, action should be taken to increase awareness of appropriate diagnostic criteria and management guidelines for actinomycetes diseases. Furthermore, an increase in the number as well as the quality of national and regional reference laboratories may facilitate more accurate diagnosis of actinomycetes diseases.
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Affiliation(s)
- Davood Azadi
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran.,Molecular Medicine Research Center, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Tahereh Motallebirad
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Kazem Ghaffari
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Dariuosh Shokri
- Department of Biology and Microbiology, Shahid Ashrafi Isfahani University, Isfahan, Iran
| | - Fatemeh Rezaei
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
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Carpentieri-Pipolo V, de Almeida Lopes KB, Degrassi G. Phenotypic and genotypic characterization of endophytic bacteria associated with transgenic and non-transgenic soybean plants. Arch Microbiol 2019; 201:1029-1045. [PMID: 31111187 DOI: 10.1007/s00203-019-01672-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 02/03/2023]
Abstract
Endophytic bacteria isolated from non-transgenic and transgenic Roundup Ready® glyphosate-resistant (GR) soybean plants were investigated to analyze the correspondence between phenotypic and genotypic characteristics and to determine whether or not the strains could be grouped based on the source of isolation in transgenic or non-transgenic plants, respectively. Most of the strains recovered from GR plants have shown the ability for plant growth promotion (PGP) by means of IAA production and inorganic phosphate solubilization, and 100% of the strains showed great motility (swarm or swim); in addition, 90% of the strains were able to metabolize the majority of carbon sources tested. GR soybean fields showed higher endophytes abundance than non-transgenic; however, analyzing the phylogenetic trees constructed using the partial 16SrRNA gene sequences, higher diversity was observed in non-transgenic soybean fields. Overall the majority of isolated endophytes could utilize multiple patterns of carbon sources and express resistance to antibiotics, while isolates varied widely in the PGP ability. The greater pattern and frequency of utilization of carbon sources and frequency and intensity of antibiotic resistance compared with PGP ability within the soybean endophytes community suggest that carbon sources metabolism and antibiotic resistance confer a greater relative fitness benefit than PGP ability. In conclusion, cluster analysis of the phenotypes and 16SrRNA gene sequences reveals lack of correspondence between the pattern of bacterial isolates and the transgenic character of plants, and the heterogeneity of clustering suggested that various adaptive processes, such as stress response, could have contributed to generate phenotypic variability to enhance endophytes overall fitness.
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Affiliation(s)
| | - Karla Bianca de Almeida Lopes
- Agronomy Department, Londrina State University, Rodovia Celso Garcia Cid, Pr 445 km 380, PO Box 10.011, Londrina, PR, 86057-970, Brazil
| | - Giuliano Degrassi
- IBioBA-ICGEB, International Centre for Genetic Engineering and Biotechnology, Polo Cientifico Tecnologico, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina.
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Saranathan R, Padmapriyadarsini C, Sivaramakrishnan GN, Perumal BK, Kannayan S, Joseph B, Gopalan N, Hanna LE. Pulmonary Mycobacterium kyorinense disease: A case report and review of literature. Indian J Med Microbiol 2019; 37:127-131. [PMID: 31424025 DOI: 10.4103/ijmm.ijmm_19_94] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We report here the first case of pulmonary infection due to Mycobacterium kyorinense in a 55-year-old hypertensive woman treated for pulmonary tuberculosis earlier on two occasions. She presented with productive cough, intermittent episode of left-sided chest pain, loss of appetite, low-grade fever, and breathlessness. Sputum cultures revealed non-tuberculous mycobacteria (NTM). She remained persistently symptomatic with sputum cultures positive for acid-fast bacilli even after 6 months of treatment. Hence, a 16SrRNA gene amplification and sequencing were done that revealed M. kyorinense. Based on the guidelines of the American Thoracic Society, she was started on weight-based dosing of clarithromycin, levofloxacin, ethambutol, isoniazid and injection amikacin daily. The patient improved symptomatically and became culture-negative after 3 months of therapy with the above regimen and continued to be culture negative for 12 months of treatment. She continues to remain symptom-free without evidence of any clinical or bacteriological relapse.
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Affiliation(s)
- Rajagopalan Saranathan
- Department of HIV, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | | | | | - Bhavani K Perumal
- Department of Clinical Research, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Silambuchelvi Kannayan
- Department of Bacteriology, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Bency Joseph
- Department of Clinical Research, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Narendran Gopalan
- Department of Clinical Research, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Luke Elizabeth Hanna
- Department of HIV, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
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Sagarduy M, Courtois S, Del Campo A, Garmendia JM, Petrau A. Differential decay and prediction of persistence of Enterococcus spp. and Escherichia coli culturable cells and molecular markers in freshwater and seawater environments. Int J Hyg Environ Health 2019; 222:695-704. [PMID: 31097324 DOI: 10.1016/j.ijheh.2019.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022]
Abstract
To quantify the impact of fecal pollution on the microbiological bathing water quality, predictive modeling is being increasingly used in which the decay rate of the fecal indicators plays an important role. The decay of sewage-sourced enterococci and Escherichia coli culturable cells and their associated molecular markers (16SrRNA) quantified by Quantitative Reverse transcription PCR were measured in controlled microcosms as well in in situ conditions using different water types, from marine waters to fresh waters with intermediate salinity. All bacterial decays were fitted to a first order decay model. In the laboratory study, the light radiation was the most influent factor affecting E. coli and enterococci survival by culture methods although environmental conditions weakly impacted the decay of molecular markers. The results also indicated differential persistence of genetic markers and culturable organisms of fecal indicator bacteria in different water systems. For each bacteria indicator and analytical method, four equations were obtained to predict the time required to have a 90% reduction (T90) according irradiance, salinity and temperature parameters. The weighted model RMSE (Root Mean Square Error) calculated for all field experiments showed that quantification obtained with the equations defined by laboratory-based study compared reasonably well with in-situ observed quantification (0.4 and 0.2 log by standard culture methods for E. coli and Enterococcus spp. and 0.6 and 0.3 log by RT-qPCR for E. coli and Enterococcus spp. respectively). The modeling tool can be used to predict the presence of fecal pollution in marine and fresh waters in combination with either culture based- or rapid molecular methods.
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Affiliation(s)
- Maialen Sagarduy
- Rivages Pro Tech, 2, Allée Théodore Monod, 64210, Bidart, France.
| | - Sophie Courtois
- Suez, CIRSEE, 38 rue du président Wilson, 78230, Le Pecq, France
| | - Andrea Del Campo
- AZTI Tecnalia, Herrera Kaia - Portualdea z/g, E-20110, Pasaia, Spain
| | | | - Agnès Petrau
- Rivages Pro Tech, 2, Allée Théodore Monod, 64210, Bidart, France
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West NJ, Parrot D, Fayet C, Grube M, Tomasi S, Suzuki MT. Marine cyanolichens from different littoral zones are associated with distinct bacterial communities. PeerJ 2018; 6:e5208. [PMID: 30038864 PMCID: PMC6054067 DOI: 10.7717/peerj.5208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/20/2018] [Indexed: 11/20/2022] Open
Abstract
The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen species Lichina pygmaea and Lichina confinis, and the maritime chlorolichen species Xanthoria aureola which occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. The L. confinis and L. pygmaea communities were significantly different from those of the maritime Xanthoria aureola lichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notably Sphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the two Lichina species were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes genera Rubricoccus, Tunicatimonas and Lewinella, suggesting an important role of these species in the marine Lichina lichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.
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Affiliation(s)
- Nyree J. West
- Observatoire Océanologique de Banyuls sur mer, Sorbonne Université, CNRS, Banyuls sur mer, France
| | - Delphine Parrot
- Univ Rennes, CNRS, ISCR—UMR 6226, Rennes, France
- Current address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine Natural Products Chemistry, GEOMAR Centre for Marine Biotechnology, Kiel, Germany
| | - Claire Fayet
- Observatoire Océanologique de Banyuls sur mer, Sorbonne Université, CNRS, Banyuls sur mer, France
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | | | - Marcelino T. Suzuki
- Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Sorbonne Université, CNRS, Banyuls sur mer, France
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Bell CR, Wilkinson JE, Robertson BK, Javan GT. Sex-related differences in the thanatomicrobiome in postmortem heart samples using bacterial gene regions V1-2 and V4. Lett Appl Microbiol 2018; 67:144-153. [PMID: 29747223 DOI: 10.1111/lam.13005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 12/27/2022]
Abstract
Recent studies have revealed distinct thanatomicrobiome (microbiome of death) signatures in human body sites after death. Thanatomicrobiome studies suggest that microbial succession after death may have the potential to reveal important postmortem biomarkers for the identification of time of death. We surveyed the postmortem microbiomes of cardiac tissues from 10 corpses with varying times of death (6-58 h) using amplicon-based sequencing of the 16S rRNA gene' V1-2 and V4 hypervariable regions. The results demonstrated that amplicons had statistically significant (P < 0·05) sex-dependent changes. Clostridium sp., Pseudomonas sp., Pantoea sp. and Streptococcus sp. had the highest enrichment for both V1-2 and V4 regions. Interestingly, the results also show that V4 amplicons had higher abundance of Clostridium sp. and Pseudomonas sp. in female hearts compared to males. In addition, Streptococcus sp. was solely found in male heart samples. The distinction between sexes was further supported by principle coordinate analysis, which revealed microbes in female hearts formed a distinctive cluster separate from male cadavers for both hypervariable regions. This study provides data that demonstrates that two hypervariable regions show discriminatory power for sex differences in postmortem heart samples. SIGNIFICANCE AND IMPACT OF THE STUDY The findings represent preliminary data of the first thanatomicrobiome investigation of a comparison between 16S rRNA gene V1-2 and V4 amplicon signatures in corpse heart tissues. The results demonstrated that V4 hypervariable region amplicons had statistically significant (P < 0·05) sex-dependent microbial diversity. For example, Streptococcus sp. was solely found in male postmortem heart tissues. Interestingly, the results also show that V4 amplicons had higher abundance of Clostridium sp. and Pseudomonas sp. in female heart tissues compared to males. The finding of Clostridium sp. supports the postmortem clostridium effect in corpse heart tissues.
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Affiliation(s)
- C R Bell
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| | - J E Wilkinson
- RTL Genomics, Research and Testing Laboratory, Lubbock, TX, USA
| | - B K Robertson
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| | - G T Javan
- Forensic Science Program, Department of Physical Sciences, Alabama State University, Montgomery, AL, USA
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Chen J, Zhang H, Wu X, Shang S, Yan J, Chen Y, Zhang H, Tang X. Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi). AMB Express 2017; 7:81. [PMID: 28413853 PMCID: PMC5392452 DOI: 10.1186/s13568-017-0374-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/21/2017] [Indexed: 02/01/2023] Open
Abstract
The gut microbiota of mammals is a complex ecosystem, which is essential for maintaining gut homeostasis and the host's health. The high throughput sequencing allowed us to gain a deeper insight into the bacterial structure and diversity. In order to improve the health status of the endangered golden takins, we first characterized the fecal microbiota of healthy golden takins using high throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions. Our results showed that, Firstly, the gut microbiota community comprised 21 phyla, 40 classes, 62 orders, 96 families, and 216 genera. Firmicutes (67.59%) was the most abundant phylum, followed by Bacteroidetes (23.57%) and Proteobacteria (2.37%). Secondly, the golden takin maintained higher richness in spring than in the winter while community diversity and evenness was not significantly different. Thirdly, four female golden takins demonstrated highly similar microbiota and the five golden takin males had relatively highly similar microbiota. All of our results might indicate that the fecal microbiota of golden takins were influenced by the season and the animal's sex. The findings provided theoretical basis regarding the gut microbiota of golden takins and may offer new insights to protect this endangered species.
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Eid NH, Al Doghaither HA, Kumosani TA, Gull M. Diversity, Physiochemical and Phylogenetic Analyses of Bacteria Isolated from Various Drinking Water Sources. Pak J Med Sci 2017; 33:703-708. [PMID: 28811799 PMCID: PMC5510131 DOI: 10.12669/pjms.333.12347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Objective: To evaluate the indigenous bacterial strains of drinking water from the most commercial water types including bottled and filtered water that are currently used in Saudi Arabia. Methods: Thirty randomly selected commercial brands of bottled water were purchased from Saudi local markets. Moreover, samples from tap water and filtered water were collected in sterilized glass bottles and stored at 4°C. Biochemical analyses including pH, temperature, lactose fermentation test (LAC), indole test (IND), methyl red test (MR), Voges-Proskauer test (VP), urease test (URE), catalase test (CAT), aerobic and anaerobic test (Ae/An) were measured. Molecular identification and comparative sequence analyses were done by full length 16S rRNA gene sequences using gene bank databases and phylogenetic trees were constructed to see the closely related similarity index between bacterial strains. Results: Among 30 water samples tested, 18 were found positive for bacterial growth. Molecular identification of four selected bacterial strains indicated the alarming presence of pathogenic bacteria Bacillus spp. in most common commercial types of drinking water used in Saudi Arabia. Conclusion: The lack of awareness about good sanitation, poor personal hygienic practices and failure of safe water management and supply are the important factors for poor drinking water quality in these sources, need to be addressed.
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Affiliation(s)
- Neveen H Eid
- Neveen H. Eid, Biochemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 42805, Jeddah, Saudi Arabia
| | - Huda A Al Doghaither
- Dr. Huda A. Al Doghaither, Biochemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 42805, Jeddah, Saudi Arabia
| | - Taha A Kumosani
- Prof. Dr. Taha A. Kumosani, Biochemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 42805, Jeddah, Saudi Arabia
| | - Munazza Gull
- Dr. Munazza Gull, Biochemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 42805, Jeddah, Saudi Arabia
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Auer L, Mariadassou M, O'Donohue M, Klopp C, Hernandez-Raquet G. Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description. Mol Ecol Resour 2017; 17:e122-e132. [PMID: 28695665 DOI: 10.1111/1755-0998.12700] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 12/01/2022]
Abstract
Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α- and β-diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering (SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α- and β-community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates.
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Affiliation(s)
- Lucas Auer
- INSA, UPS, LISBP, Université de Toulouse, Toulouse Cedex 4, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | | | - Michael O'Donohue
- INSA, UPS, LISBP, Université de Toulouse, Toulouse Cedex 4, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | | | - Guillermina Hernandez-Raquet
- INSA, UPS, LISBP, Université de Toulouse, Toulouse Cedex 4, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
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Abstract
Mitochondrial DNA (mtDNA) lacks the protection provided by the nucleosomes in the nuclear DNA and does not have a DNA repair mechanism, making it highly susceptible to damage, which can lead to mtDNA depletion. mtDNA depletion compromises the efficient function of cells and tissues and thus impacts negatively on health. Here, we describe a brief and easy protocol to quantify mtDNA copy number by determining the mtDNA/nDNA ratio. The procedure has been validated using a cohort of young and aged mice. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Pedro M Quiros
- Laboratory for Integrative and Systems Physiology, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Aashima Goyal
- Laboratory for Integrative and Systems Physiology, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Pooja Jha
- Laboratory for Integrative and Systems Physiology, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory for Integrative and Systems Physiology, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
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43
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Zhao MM, Du SS, Li QH, Chen T, Qiu H, Wu Q, Chen SS, Zhou Y, Zhang Y, Hu Y, Su YL, Shen L, Zhang F, Weng D, Li HP. High throughput 16SrRNA gene sequencing reveals the correlation between Propionibacterium acnes and sarcoidosis. Respir Res 2017; 18:28. [PMID: 28143482 PMCID: PMC5286795 DOI: 10.1186/s12931-017-0515-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/19/2017] [Indexed: 02/01/2023] Open
Abstract
Objective This study aims to use high throughput 16SrRNA gene sequencing to examine the bacterial profile of lymph node biopsy samples of patients with sarcoidosis and to further verify the association between Propionibacterium acnes (P. acnes) and sarcoidosis. Methods A total of 36 mediastinal lymph node biopsy specimens were collected from 17 cases of sarcoidosis, 8 tuberculosis (TB group), and 11 non-infectious lung diseases (control group). The V4 region of the bacterial 16SrRNA gene in the specimens was amplified and sequenced using the high throughput sequencing platform MiSeq, and bacterial profile was established. The data analysis software QIIME and Metastats were used to compare bacterial relative abundance in the three patient groups. Results Overall, 545 genera were identified; 38 showed significantly lower and 29 had significantly higher relative abundance in the sarcoidosis group than in the TB and control groups (P < 0.01). P. acnes 16SrRNA was exclusively found in all the 17 samples of the sarcoidosis group, whereas was not detected in the TB and control groups. The relative abundance of P. acnes in the sarcoidosis group (0.16% ± 0. 11%) was significantly higher than that in the TB (Metastats analysis: P = 0.0010, q = 0.0044) and control groups (Metastats analysis: P = 0.0010, q = 0.0038). The relative abundance of P. granulosum was only 0.0022% ± 0. 0044% in the sarcoidosis group. P. granulosum 16SrRNA was not detected in the other two groups. Conclusion High throughput 16SrRNA gene sequencing appears to be a useful tool to investigate the bacterial profile of sarcoidosis specimens. The results suggest that P. acnes may be involved in sarcoidosis development. Electronic supplementary material The online version of this article (doi:10.1186/s12931-017-0515-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng-Meng Zhao
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Shan-Shan Du
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Qiu-Hong Li
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Tao Chen
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Hui Qiu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Qin Wu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Shan-Shan Chen
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Ying Zhou
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Yuan Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Yang Hu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Yi-Liang Su
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Li Shen
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Fen Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China
| | - Dong Weng
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China.
| | - Hui-Ping Li
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, 507 Zheng Min Road, Shanghai, 200433, China.
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Abstract
In 1675, Antoni Van Leeuwenhoeck was the first to observe several forms using an optical microscope that he named "animalcules", realizing later that these were microorganisms. The first classification of living organisms proposed by Ehrenberg in 1833 was based on what we could visualize. The failure of this kind of classification arises from viral culture, which preceded direct observations that were finally achieved during the 20th century by electron microscopy. The number of prokaryotic species is estimated at approximately 10 million, although only 1800 were known in 1980, and 14,000 to date, thanks to the advent of 16S rRNA amplification and sequencing. This highlights our inability to access the entire diversity. Indeed, a large number of bacteria are only, known as Operational Taxonomic Units (OTUs) and detected as a result of metagenomics studies, revealing an unexplored world known as the "dark matter". Recently, the rebirth of bacterial culture through the example of culturomics has dramatically increased the human gut repertoire as well as the 18SrRNA sequencing allowed to largely extend the repertoire of Eukaryotes. Finally, filtration and co-culture on free-living protists associated with high-throughput culture elucidated a part of the megavirome. While the majority of studies currently performed on the human gut microbiota focus on bacterial diversity, it appears that several other prokaryotes (including archaea) and eukaryotic populations also inhabit this ecosystem; their detection depending exclusively on the tools used. Rational and comprehensive establishment of this ecosystem will allow the understanding of human health associated with gut microbiota and the potential to change this.
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Pourbakhsh SA, Abtin AR, Ashtari A, Kheirkhah B, Bayatzadeh MA, Ahangran S. Isolation and Detection of Mycoplasma agalactiae from Semen Samples of Goats. Arch Razi Inst 2016; 72:159-164. [PMID: 30341936 DOI: 10.22092/ari.2017.111610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/01/2016] [Indexed: 09/30/2022]
Abstract
Contagious agalactia (CA) is a highly infectious disease of goats and sheep, and is a form of Mycoplasmosis, which is usually enzootic. Since Mycoplasma agalactiae (M. agalactiae) is the main cause of this disease in goats, the aim of this study was to isolate and detect M. agalactiae from semen of goat bucks. Thirty-nine semen samples were collected from goat bulks, and all samples were cultured in PPLO broth medium supplemented for M. agalaciae isolation. The bacteria DNAs were extracted from clinical samples and the PCR assay was applied to detect Mycoplasma genus and M. agalactiae species using specific primers, which amplified a 163bp fragment in 16SrRNA gene and a 375bp fragment in lipoprotein gene. The PCR evaluations were performed for both the clinical samples and the cultures. Out of the 39 samples, 29 (74.3%) of the cultures were shown positive and typical Mycoplasma colonies grew on PPLO agar, which could be considered as the diagnostic method. In addition, 38 (97.4%) samples had positive PCR results for Mycoplasma genus and six (15.3%) of the samples were shown to be positive using PCR for M. agalactiae as the diagnostic method. In the present study, M. agalactiae was detected in semen of goat bulks for the first time in Iran. Therefore, it is recommended to concern semen as one of the significant sources for this pathogen and the possibility for transmission to the female goats through semen is highlighted. Moreover, presence of this microorganism in semen could be involved in infertility of goat population.
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Affiliation(s)
- S A Pourbakhsh
- Mycoplasma Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran.,Mycoplasma Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - A R Abtin
- Mycoplasma Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - A Ashtari
- Mycoplasma Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - B Kheirkhah
- Department of Microbiology, Faculty of Sciences, Islamic Azad University of Baft, Kerman, Iran
| | - M A Bayatzadeh
- Mycoplasma Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - S Ahangran
- Mycoplasma Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
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Botsaris G, Kanetis L, Slaný M, Parpouna C, Makris KC. Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus). Environ Monit Assess 2015; 187:739. [PMID: 26559553 DOI: 10.1007/s10661-015-4957-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.
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Affiliation(s)
- George Botsaris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3603, Limassol, Cyprus.
| | - Loukas Kanetis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3603, Limassol, Cyprus
| | - Michal Slaný
- Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Christiana Parpouna
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3603, Limassol, Cyprus
| | - Konstantinos C Makris
- Water and Health Laboratory, Cyprus International Institute for Environmental and Public Health in association with the Harvard School of Public Health, Cyprus University of Technology, Limassol, Cyprus
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Puillandre N, Bouchet P, Duda TF, Kauferstein S, Kohn AJ, Olivera BM, Watkins M, Meyer C. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea). Mol Phylogenet Evol 2014; 78:290-303. [PMID: 24878223 PMCID: PMC5556946 DOI: 10.1016/j.ympev.2014.05.023] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/08/2014] [Accepted: 05/16/2014] [Indexed: 11/26/2022]
Abstract
We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.
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Affiliation(s)
- N Puillandre
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB Institut (UMR 7205 CNRS/UPMC/MNHN/EPHE), 43, Rue Cuvier, 75231 Paris, France.
| | - P Bouchet
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB Institut (UMR 7205 CNRS/UPMC/MNHN/EPHE), 55, Rue Buffon, 75231 Paris, France.
| | - T F Duda
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA; Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama.
| | - S Kauferstein
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596 Frankfurt, Germany.
| | - A J Kohn
- Department of Biology, Box 351800, University of Washington, Seattle, WA 98195, USA.
| | - B M Olivera
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
| | - M Watkins
- Department of Pathology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
| | - C Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
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