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Wang Q, Zhan PC, Han XL, Lu T. Metagenomic and culture-dependent analysis of Rhinopithecius bieti gut microbiota and characterization of a novel genus of Sphingobacteriaceae. Sci Rep 2024; 14:13819. [PMID: 38879636 PMCID: PMC11180105 DOI: 10.1038/s41598-024-64727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/12/2024] [Indexed: 06/19/2024] Open
Abstract
Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009T, formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009T and its most closely related strains S. kitahiroshimense 10CT, S. pakistanense NCCP-246T and S. faecium DSM 11690T were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009T represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009T = CCTCC AA 2021153T = KCTC 82941T) are proposed.
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Affiliation(s)
- Qiong Wang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
- Center for Pharmaceutical Sciences, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, PR China
| | - Peng-Chao Zhan
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
| | - Xiu-Lin Han
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
| | - Tao Lu
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
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El-Toukhy SE, El-Daly SM, Kamel MM, Nabih HK. The diagnostic significance of circulating miRNAs and metabolite profiling in early prediction of breast cancer in Egyptian women. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04492-2. [DOI: 10.1007/s00432-022-04492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
Abstract
Objective
Breast cancer (BC) is one of the most commonly diagnosed solid malignancies in women worldwide.
Purpose
Finding new non-invasive circulating diagnostic biomarkers will facilitate the early prediction of BC and provide valuable insight into disease progression and response to therapy using a safe and more accessible approach available every inspection time. Therefore, our present study aimed to investigate expression patterns of potentially circulating biomarkers that can differentiate well between benign, malignant, and healthy subjects.
Methods
To achieve our target, quantitative analyses were performed for some circulating biomarkers which have a role in the proliferation and tumor growth, as well as, glutamic acid, and human epidermal growth receptor 2 (HER2) in blood samples of BC patients in comparison to healthy controls using qRT-PCR, liquid chromatography/mass spectrometry (LC/MS/MS), and ELISA.
Results
Our findings showed that the two miRNAs (miRNA-145, miRNA-382) were expressed at lower levels in BC sera than healthy control group, while miRNA-21 was expressed at higher levels in BC patients than control subjects. Area under ROC curves of BC samples revealed that AUC of miRNA-145, miRNA-382, miRNA-21, and glutamic acid was evaluated to equal 0.99, 1.00, 1.00 and 1.00, respectively. Besides, there was a significantly positive correlation between miRNA-145 and miRNA-382 (r = 0.737), and a highly significant positive correlation between miRNA-21 and glutamic acid (r = 0.385).
Conclusion
Based on our results, we conclude that the detection of serum miRNA-145, -382 and -21 as a panel along with glutamic acid, and circulating HER2 concentrations could be useful as a non-invasive diagnostic profiling for early prediction of breast cancer in Egyptian patients. It can provide an insight into disease progression, discriminate between malignancy and healthy control, and overcome the use limitations (low sensitivity and specificity, repeated risky exposure, and high cost) of other detecting tools, including mammography, magnetic resonance imaging, and ultrasound.
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Ayvaz H, Temizkan R, Menevseoglu A, Dogan MA, Nazlim BA, Gunay E, Uysal Pala C. A comprehensive study on the quality characteristics of sweet red pepper paste and the evaluation of near-infrared spectroscopy as a rapid alternative tool. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-04156-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bruce SA, Aytur SA, Andam CP, Bucci JP. Metagenomics to characterize sediment microbial biodiversity associated with fishing exposure within the Stellwagen Bank National Marine Sanctuary. Sci Rep 2022; 12:9499. [PMID: 35680904 PMCID: PMC9184631 DOI: 10.1038/s41598-022-13409-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
Abstract
Microbes in marine sediments constitute a large percentage of the global marine ecosystem and function to maintain a healthy food web. In continental shelf habitats such as the Gulf of Maine (GoM), relatively little is known of the microbial community abundance, biodiversity, and natural product potential. This report is the first to provide a time-series assessment (2017–2020) of the sediment microbial structure in areas open and closed to fishing within the Stellwagen Bank National Marine Sanctuary (SBNMS). A whole metagenome sequencing (WMS) approach was used to characterize the sediment microbial community. Taxonomic abundance was calculated across seven geographic sites with 14 individual sediment samples collected during the summer and fall seasons. Bioinformatics analyses identified more than 5900 different species across multiple years. Non-metric multidimensional scaling methods and generalized linear models demonstrated that species richness was inversely associated with fishing exposure levels and varied by year. Additionally, the discovery of 12 unique biosynthetic gene clusters (BGCs) collected across sites confirmed the potential for medically relevant natural product discovery in the SBNMS. This study provides a practical assessment of how fishing exposure and temporal trends may affect microbial community structure in a coastal marine sanctuary.
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Affiliation(s)
- Spencer A Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Semra A Aytur
- Department of Health Management & Policy, University of New Hampshire, Durham, NH, 03824, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - John P Bucci
- School of Marine Science & Ocean Engineering, University of New Hampshire, Durham, NH, 03824, USA. .,Marine Microverse Institute, Kittery Point, ME, 03905, USA.
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Saawarn B, Hait S. Occurrence, fate and removal of SARS-CoV-2 in wastewater: Current knowledge and future perspectives. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:104870. [PMID: 33282675 PMCID: PMC7706426 DOI: 10.1016/j.jece.2020.104870] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/12/2020] [Accepted: 11/29/2020] [Indexed: 05/03/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a pandemic of global concern, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, many studies have documented the detection of SARS-CoV-2 in human excreta and wastewater. The presence of SARS-CoV-2 in human excreta and wastewater poses serious implications for wastewater treatment. Thus, this review aims to understand the fate of SARS-CoV-2 in the urban water cycle and its inactivation in different stages of treatment in wastewater treatment plants (WWTPs) for effective control to prevent any recurrence of the outbreak. The viral load of SARS-CoV-2 in feces of individuals tested positive has been reported to be in the range of 104-108 copies/L depending on the infection stages. In the wastewater, dilution of feces results in the decrease of the viral load in the range of 102-106.5 copies/L. Monitoring of SARS-CoV-2 in WWTP samples following the wastewater-based epidemiology (WBE) can complement real epidemiological data from clinical testing to help to monitor disease outbreaks in a community. Though promising, high uncertainty involved with the WBE technique warrants further research for reliable and quantitative information. Inactivation of SARS-CoV-2 in WWTPs depends on the operational parameters and is generally enhanced by the tertiary treatment and disinfection techniques with a higher dosage. However, the risk of SARS-CoV-2 dissemination by the treated effluent intended to be disposed of or reused in the urban water cycle needs to be assessed with respect to the extent of viral infectivity.
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Affiliation(s)
- Bhavini Saawarn
- Department of Civil and Environmental Engineering, Indian Institute of Technology Patna, Bihar 801 106, India
| | - Subrata Hait
- Department of Civil and Environmental Engineering, Indian Institute of Technology Patna, Bihar 801 106, India
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Baldachini M, Regaiolli B, Llorente M, Riba D, Spiezio C. The Influence of Target Animacy and Social Rank on Hand Preference in Barbary Macaques (Macaca sylvanus). INT J PRIMATOL 2021. [DOI: 10.1007/s10764-020-00193-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Narayanan S, Blumberg B, Clayman ML, Pan V, Wicklund C. Exploring the Issues Surrounding Clinical Exome Sequencing in the Prenatal Setting. J Genet Couns 2018. [DOI: 10.1007/s10897-018-0245-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rohwer S, Rohwer VG. Breeding and multiple waves of primary molt in common ground doves of coastal Sinaloa. PeerJ 2018; 6:e4243. [PMID: 29379683 PMCID: PMC5787347 DOI: 10.7717/peerj.4243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/18/2017] [Indexed: 11/24/2022] Open
Abstract
For adult Common Ground Doves from Sinaloa we demonstrate that the primaries are a single molt series, which sometimes feature two (in one case three) waves of feather replacement. Such stepwise primary replacement is found in many large birds but, at 40 g, this dove is much the smallest species reported to have multiple waves of replacement proceeding through its primaries simultaneously. Pre-breeding juvenile Common Ground Doves never feature two waves of primary replacement. Juveniles usually have more than two adjacent feathers growing simultaneously and replace their primaries in about 100 days. In contrast adults, which extensively overlap molt and breeding, usually grow just a single primary at a time, and require at least 145 days to replace their primaries. Molt arrests are thought to drive the generation of new waves of primary replacement in a diversity of large birds. For adult Common Ground Doves, we found molt arrests to be strongly associated with active crop glands, suggesting that the demands of parental care cause arrests in primary replacement in this dove. For those adults with two primary molt waves, initiation of an inner wave was most frequently observed once the outer wave had reached P10. Thus, unlike reports for large birds, Common Ground Doves usually suppress the initiation of a new wave of molt starting at P1 when the preceding wave arrests before reaching the distal primaries. This assures that relatively fresh inner primaries are not replaced redundantly, overcoming a serious flaw in stepwise molting in large birds (Rohwer, 1999).
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Affiliation(s)
- Sievert Rohwer
- Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, WA, United States of America
| | - Vanya G Rohwer
- Museum of Vertebrates, Cornell University, Ithaca, NY, United States of America
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