1
|
Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N, Tangkijvanich P. Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma. Appl Microbiol Biotechnol 2024; 108:34. [PMID: 38183473 PMCID: PMC10771587 DOI: 10.1007/s00253-023-12845-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 01/08/2024]
Abstract
Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). Fecal specimens were obtained from 16 healthy controls, 33 patients with viral-HCC (17 and 16 cases with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, respectively), and 18 patients with NBNC-HCC. Compositions of fecal microbiota were assessed by 16S rRNA sequencing. Bioinformatic analysis was performed by the DADA2 pipeline in the R program. Significantly different genera from the top 50 relative abundance were used to classify between subgroups of HCC by the Random Forest algorithm. Our data demonstrated that the HCC group had a significantly decreased alpha-diversity and changed microbial composition in comparison with healthy controls. Within the top 50 relative abundance, there were 11 genera including Faecalibacterium, Agathobacter, and Coprococcus that were significantly enhanced in Viral-HCC, while 5 genera such as Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium were enhanced in NBNC-HCC. Compared to Viral-HCC, the NBNC-HCC subgroup significantly reduced various short-chain fatty acid-producing bacteria, as well as declined fecal butyrate but elevated plasma surrogate markers of microbial translocation. Based on the machine learning algorithm, a high diagnostic accuracy to classify HCC subgroups was achieved with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.94. Collectively, these data revealed that gut dysbiosis was distinct according to etiological factors of HCC, which might play an essential role in hepatocarcinogenesis. These findings underscore the possible use of a gut microbiota signature for the diagnosis and therapeutic approaches regarding different subgroups of HCC. KEY POINTS: • Gut dysbiosis is connected to hepatocarcinogenesis and can be used as a novel biomarker. • Gut microbiota composition is significantly altered in different etiological factors of HCC. • Microbiota-based signature can accurately distinguish between Viral-HCC and NBNC-HCC.
Collapse
Affiliation(s)
- Thananya Jinato
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Doctor of Philosophy Program in Medical Sciences, Graduate Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Songtham Anuntakarun
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nantawat Satthawiwat
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| |
Collapse
|
2
|
Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [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: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
Collapse
Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| |
Collapse
|
3
|
Jachimowicz P, Mądzielewska W, Cydzik-Kwiatkowska A. Microplastics in granular sequencing batch reactors: Effects on pollutant removal dynamics and the microbial community. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135061. [PMID: 38972205 DOI: 10.1016/j.jhazmat.2024.135061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/09/2024]
Abstract
This study investigated the relationship between microplastic (MP) presence and pollutant removal in granular sludge sequencing batch reactors (GSBRs). Two types of MPs, polyethylene (PE) and polyethylene terephthalate (PET), were introduced in varying concentrations to assess their effects on microbial community dynamics and rates of nitrogen, phosphorus, and organic compound removal. The study revealed type-dependent variations in the deposition of MPs within the biomass, with PET-MPs exhibiting a stronger affinity for accumulation in biomass. A 50 mg/L dose of PET-MP decreased COD removal efficiency by approximately 4 % while increasing P-PO4 removal efficiency by around 7 % compared to the control reactor. The rate of nitrogen compounds removal decreased with higher PET-MP dosages but increased with higher PE-MP dosages. An analysis of microbial activity and gene abundance highlighted the influence of MPs on the expression of the nosZ and ppk1 genes, which code enzymes responsible for nitrogen and phosphorus transformations. The study also explored shifts in microbial community structure, revealing alterations with changes in MP dose and type. This research contributes valuable insights into the complex interactions between MP, microbial communities, and pollutant removal processes in GSBR systems, with implications for the sustainable management of wastewater treatment in the presence of MP.
Collapse
Affiliation(s)
- Piotr Jachimowicz
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-709 Olsztyn, Poland.
| | - Weronika Mądzielewska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-709 Olsztyn, Poland
| | - Agnieszka Cydzik-Kwiatkowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-709 Olsztyn, Poland
| |
Collapse
|
4
|
Pelpolage SW, Kobayashi H, Fukuma N, Hoshizawa M, Hamamoto T, Han KH, Fukushima M. Temporal changes in the fermentation characteristics, bacterial community structure and the functionality of the predicted metagenome of a batch fermenter medium containing the upper gastrointestinal enzyme resistant fraction of white sorghum (Sorghum bicolor L. Moench). Food Chem 2024; 448:139102. [PMID: 38593566 DOI: 10.1016/j.foodchem.2024.139102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Sorghum is a potential prebiotic ascribed to the high native resistant starch (RS) content. Our previous studies on raw sorghum have revealed prominent amino acid fermentation despite the high RS content. Interestingly, autoclaved-freeze-dried sorghum fed rats exhibited beneficial microbial and biochemical profiles. Having a keen interest to reciprocally scrutinize the underlying mechanisms behind these contrasting outcomes, we used an in vitro porcine batch fermentation model. The fermentable substrates in raw and autoclaved-freeze-dried (three cycles) sorghum (AC) after in vitro gastrointestinal digestion fostered similar bacterial community structures, yet with significant differences in the characteristic amylolytic microbial taxa abundance and their temporal variation. Further, significant differences in the concentration of organic acids in raw and AC manifested the differences in the predicted abundance of the underlying pathways of carbohydrate and organic acid metabolism. Thus, this study highlights the propensity of the heat-moisture treatment of sorghum in modifying the fermentability of its RS.
Collapse
Affiliation(s)
- Samanthi W Pelpolage
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555, Hokkaido, Japan.
| | - Haruhi Kobayashi
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555, Hokkaido, Japan.
| | - Naoki Fukuma
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555, Hokkaido, Japan; Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555., Hokkaido, Japan.
| | - Michiyo Hoshizawa
- U.S. Grains Council, 11th Floor, Toranomon Denki Building No.3, 1-2-20 Toranomon, Minato-ku, Tokyo 105-0001, Japan.
| | - Tetsuo Hamamoto
- U.S. Grains Council, 11th Floor, Toranomon Denki Building No.3, 1-2-20 Toranomon, Minato-ku, Tokyo 105-0001, Japan.
| | - Kyu-Ho Han
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555, Hokkaido, Japan; Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555., Hokkaido, Japan.
| | - Michihiro Fukushima
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, West 2-11, Inada, Obihiro 080-8555, Hokkaido, Japan.
| |
Collapse
|
5
|
Núñez-Montero K, Leal K, Rojas-Villalta D, Castro M, Larronde C, Wagenknecht L, Contreras MJ. 16s gene metagenomic characterization in healthy stallion semen. Res Vet Sci 2024; 176:105354. [PMID: 38981836 DOI: 10.1016/j.rvsc.2024.105354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
Studies on the bacterial composition of seminal samples have primarily focused on species isolated from semen and their effects on fertility and reproductive health. Culture-independent techniques, such as 16S rRNA gene sequencing and shotgun metagenomics, have revolutionized our ability to identify unculturable bacteria, which comprise >90% of the microbiome. These techniques allow for comprehensive analysis of microbial communities in seminal samples, shedding light on their interactions and roles. In this study, we characterized the taxonomic diversity of seminal microbial communities in healthy stallions using 16S rRNA gene sequencing. Semen samples were collected from four stallions during the reproductive season, and DNA was extracted for sequencing. The results revealed a diverse array of bacterial taxa, with Firmicutes, Bacteroidota, and Proteobacteria being predominant phyla. At the family and genus levels, significant variations were observed among individuals, with individual variability in microbial richness and diversity standing out. Moreover, each stallion showed a distinct microbial fingerprint, indicating the presence of a characteristic microbial core for each stallion. These results underscore the importance of considering individual microbial profiles in understanding reproductive health and fertility outcomes.
Collapse
Affiliation(s)
- Kattia Núñez-Montero
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Temuco 4810101, Chile
| | - Karla Leal
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco 4810101, Chile
| | - Dorian Rojas-Villalta
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Macarena Castro
- Doctorado en Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco 4810101, Chile
| | - Carolina Larronde
- Facultad de La Salud, Universidad Autónoma de Chile, Temuco 4810101, Chile
| | | | - María José Contreras
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco 4810101, Chile.
| |
Collapse
|
6
|
Thomsen M, Vemuri R, Huygens F, Clarke S, Vitetta L. An exploratory study of a multi-species probiotic formulation and markers of health in a real-world oncological cohort in the time of covid. Inflammopharmacology 2024; 32:2317-2335. [PMID: 38926298 PMCID: PMC11300539 DOI: 10.1007/s10787-024-01503-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION The efficacy of cancer treatments has links to the intestinal microbiome. Mucositis is a dose-limiting intestinal pro-inflammatory side effect of cancer treatments, that increases the risk of diarrhoea, mucositis, and in severe cases, febrile neutropenia. METHODS The effect of cancer treatments on Quality of Life (QoL) was assessed using the FACT C questionnaire that included patient wellbeing and gut adverse symptoms (e.g. diarrhoea). Participants rated faecal samples via the Bristol Stool Chart. In addition, bacterial DNA was extracted from faecal samples, sequenced, and taxonomically examined. The incidence / severity of neutropenia was assessed with white blood cell and neutrophil counts. Circulating SCFAs and plasma lipopolysaccharide (LPS) endotoxin levels were recorded and correlated to intestinal mucositis. RESULTS Improvement in bowel function, with reduction in constipation and or diarrhoea or absence of significant disturbance to bowel function was recorded in 85% of the participants. One participant developed febrile neutropenia and two developed bowel toxicity during the study, that was unrelated to the test formulation. No significant changes in microbiota alpha- and beta-diversity at the phylum and species levels respectively from baseline to end of study treatment was observed. None of the participants had raised plasma-endotoxin levels from baseline to the first and subsequent treatment cycles for their cancers. Probiotics in this cohort were deemed safe and tolerable. Significant improvement in emotional QoL scores (p = 0.015) was reported with increased number of chemotherapy cycles. In a related observational study of exceptional responders to chemotherapy, participants were found to have had a high intake of fruits, vegetables, and fibre possibly indicative of a more balanced intestinal microbiota. CONCLUSION A multi-strain probiotic formulation was safe and tolerated in this chronically ill cohort that were undergoing oncological treatment. The probiotic formulation alleviated diarrhoea, constipation and maintained stool consistency/frequency during the multiple treatments with chemotherapy and radiotherapy. Intestinal dysbiosis that is characterised by decreased microbial diversity and increased pro-inflammatory species was not observed. Probiotic supplementation may have helped reduce dysbiosis during cancer treatments. These improvements may have been critical with the observation that emotional wellbeing was significantly improved from baseline. Hence albeit that the study had limitations, the probiotic intervention provided adjunctive treatment support to the patients. What is of scientifically plausible interest is that probiotics have a long association historically with human hosts and as such ratify their inclusion offering a significant adjunctive therapeutic potential. Future studies warrant larger sample sizes, control groups and should limit recruitment to a largely homogenous group of patients.
Collapse
Affiliation(s)
- Michael Thomsen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, Sydney, NSW, 2006, Australia
| | - Ravichandra Vemuri
- School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Flavia Huygens
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Stephen Clarke
- Faculty of Medicine and Health, The University of Sydney, Camperdown, Sydney, NSW, 2006, Australia
| | - Luis Vitetta
- Faculty of Medicine and Health, The University of Sydney, Camperdown, Sydney, NSW, 2006, Australia.
| |
Collapse
|
7
|
Kolenc Ž, Kovač Viršek M, Klančnik A, Janecko N. Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175130. [PMID: 39084364 DOI: 10.1016/j.scitotenv.2024.175130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m3 water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.
Collapse
Affiliation(s)
- Živa Kolenc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Manca Kovač Viršek
- Institute for Water of the Republic of Slovenia, Einspielerjeva ulica 6, 1000 Ljubljana, Slovenia; Geological Survey of Slovenia, Dimičeva ulica 14, 1000 Ljubljana, Slovenia
| | - Anja Klančnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
| | - Nicol Janecko
- Quadram Institute Bioscience, Rosalind Franklin Rd, Norwich Research Park, Norwich NR4 7UQ, UK
| |
Collapse
|
8
|
Garibay-Valdez E, Olivas-Bernal CA, Vargas-Albores F, Martínez-Porchas M, García-Godínez DM, Medina-Félix D, Martínez-Córdova LR, Cicala F. Deciphering the gut microbiota of zebrafish, the most used fish as a biological model: A meta-analytic approach. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111713. [PMID: 39074543 DOI: 10.1016/j.cbpa.2024.111713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
A meta-analytic approach deciphered the taxonomic profile of the zebrafish gut microbiota at different developmental stages. Data (16S rDNA) were systematically searched in databases, selecting those with intestine samples of fish not exposed to a particular treatment or challenge (e.g., pathogens, dietetic tests, xenobiotics, etc.) and obtaining 340 samples to be processed. Results revealed marked differences between the developmental phases. Proteobacteria was the dominant phylum in the larval phase, with a relative abundance of 90%, while the rest of the phyla did not exceed 2%. Vibrio, Aeromonas, Plesiomonas, Pseudomonas, Shewanella, and Acinetobacter were the dominant genera in this phase. Transitional changes were observed after the larvae stage. Proteobacteria still registered high abundance (48%) in the juvenile phase, but Fusobacteria (40%) and Bacteriodota (5.9%) registered considerable increases. Genera, including Cetobacterium, Plesiomonas, Aeromonas, Vibrio, and Flavobacterium, dominated this stage. The phyla Proteobacteria (48%) and Fusobacteria (35%) were strongly established in the adult phase. Cetobacterium was registered as the most abundant genus, followed by Aeromonas, Acinetobacter, Plesiomonas, Vibrio, and ZOR0006 (Firmicutes; 6%). In conclusion, the composition of the intestinal microbiota of zebrafish is consistently determined by two primary phyla, Proteobacteria and Fusobacteria; however, this composition varies depending on the developmental stage. Cetobacterium and Aeromonas are the most relevant genera in juveniles and adults. Finally, these results reveal a consistent pattern of certain bacterial groups in the zebrafish microbiota that could help shape gnotobiotic models (colonized with a specific known bacterial community) or synthetic microbiota (in vitro assembly of microbes), among other approaches.
Collapse
Affiliation(s)
- Estefanía Garibay-Valdez
- Biology of Aquatic Organisms, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | | | - Francisco Vargas-Albores
- Biology of Aquatic Organisms, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Marcel Martínez-Porchas
- Biology of Aquatic Organisms, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.
| | | | | | - Luis Rafael Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Francesco Cicala
- IRSA Verbania, Consiglio Nazionale delle Ricerche-Verbania, Italy
| |
Collapse
|
9
|
Lin JH, Lin CH, Kuo YW, Liao CA, Chen JF, Tsai SY, Li CM, Hsu YC, Huang YY, Hsia KC, Yeh YT, Ho HH. Probiotic Lactobacillus fermentum TSF331, Lactobacillus reuteri TSR332, and Lactobacillus plantarum TSP05 improved liver function and uric acid management-A pilot study. PLoS One 2024; 19:e0307181. [PMID: 39046973 PMCID: PMC11268587 DOI: 10.1371/journal.pone.0307181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/30/2024] [Indexed: 07/27/2024] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is predominantly associated with metabolic disturbances representing aberrant liver function and increased uric acid (UA) levels. Growing evidences have suggested a close relationship between metabolic disturbances and the gut microbiota. A placebo-controlled, double-blinded, randomized clinical trial was therefore conducted to explore the impacts of daily supplements with various combinations of the probiotics, Lactobacillus fermentum TSF331, Lactobacillus reuteri TSR332, and Lactobacillus plantarum TSP05 with a focus on liver function and serum UA levels. Test subjects with abnormal levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and UA were recruited and randomly allocated into six groups. Eighty-two participants successfully completed the 60-day intervention without any dropouts or occurrence of adverse events. The serum AST, ALT, and UA levels were significantly reduced in all treatment groups (P < 0.05). The fecal microbiota analysis revealed the intervention led to an increase in the population of commensal bacteria and a decrease in pathobiont bacteria, especially Bilophila wadsworthia. The in vitro study indicated the probiotic treatments reduced lipid accumulation and inflammatory factor expressions in HepG2 cells, and also promoted UA excretion in Caco-2 cells. The supplementation of multi-strain probiotics (TSF331, TSR332, and TSP05) together can improve liver function and UA management and may have good potential in treating asymptomatic MAFLD. Trial registration. The trial was registered in the US Library of Medicine (clinicaltrials.gov) with the number NCT06183801 on December 28, 2023.
Collapse
Affiliation(s)
- Jia-Hung Lin
- Functional R&D Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Chi-Huei Lin
- Functional R&D Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Yi-Wei Kuo
- Functional R&D Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Chorng-An Liao
- Aging and Disease Prevention Research Center, Fooyin University, Kaohsiung City, Taiwan
| | - Jui-Fen Chen
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Shin-Yu Tsai
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Ching-Min Li
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Yu-Chieh Hsu
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Yen-Yu Huang
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Ko-Chiang Hsia
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| | - Yao-Tsung Yeh
- Aging and Disease Prevention Research Center, Fooyin University, Kaohsiung City, Taiwan
- Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung City, Taiwan
| | - Hsieh-Hsun Ho
- Functional R&D Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
- Research Product Department, Research and Design Center, Glac Biotech Co., Ltd., Tainan City, Taiwan
| |
Collapse
|
10
|
Zhang W, Zheng L, Xie J, Su X, Zhang M, Huang H, Schmitz-Esser S, Du S, Yang Y, Xie J, Zhang Q, Yu S, Guo Q, Wang H, Zhang L, Yang K, Hou R. The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline. mSystems 2024; 9:e0052024. [PMID: 38920380 PMCID: PMC11265448 DOI: 10.1128/msystems.00520-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Some lactic acid bacteria (LAB) can provide significant health benefits, which are critically important for the conservation of endangered animals, such as giant pandas. However, little is known about the diversity and culturability of LAB in the giant panda gut microbiota. To understand the roles of LAB in giant panda conservation, it is critical to culture bacterial strains of interest. In this study, we established a pipeline to culture bacterial strains using enrichment of target bacteria with different liquid media and growth conditions. Then, the strains were isolated in solid media to study their functions. Using 210 samples from the culture enrichment method and 138 culture-independent samples, we obtained 1120 amplicon sequencing variants (ASVs) belonging to Lactobacillales. Out of the 1120 ASVs, 812 ASVs from the culture enrichment approach were twofold more diverse than 336 ASVs from the culture-independent approach. Many ASVs of interest were not detected in the culture-independent approach. Using this pipeline, we isolated many relevant bacterial strains and established a giant panda gut bacteria strain collection that included strains with low-abundance in culture-independent samples and included most of the giant panda LAB described by other researchers. The strain collection consisted of 60 strains representing 35 species of 12 genera. Thus, our pipeline is powerful and provides guidance in culturing gut microbiota of interest in hosts such as the giant panda.IMPORTANCECultivation is necessary to screen strains to experimentally investigate microbial traits, and to confirm the activities of novel genes through functional characterization studies. In the long-term, such work can aid in the identification of potential health benefits conferred by bacteria and this could aid in the identification of bacterial candidate strains that can be applied as probiotics. In this study, we developed a pipeline with low-cost and user-friendly culture enrichment to reveal the diversity of LAB in giant pandas. We compared the difference between culture-independent and culture enrichment methods, screened strains of interest that produced high concentrations of short-chain fatty acids (SCFAs), and we investigated the catalog of virulence factors, antibiotic resistance, butyrate and lactate synthesis genes of the strains at a genomic level. This study will provide guidance for microbiota cultivation and a foundation for future research aiming to understand the functions of specific strains.
Collapse
Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Lijun Zheng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Junjin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Xiaoyan Su
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu, Sichuan, China
| | - He Huang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | | | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Yu Yang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Jiqin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qinrong Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Shuran Yu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qiang Guo
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Hairui Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Kong Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| |
Collapse
|
11
|
Radziemska M, Blazejczyk A, Gusiatin MZ, Cydzik-Kwiatkowska A, Majewski G, Brtnický M. Compost-diatomite-based phytostabilization course under extreme environmental conditions in terms of high pollutant contents and low temperatures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174917. [PMID: 39034003 DOI: 10.1016/j.scitotenv.2024.174917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/05/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024]
Abstract
The effects of changes in environmental temperatures on the immobilization or removal of cationic potentially toxic elements (PTE) in heavily polluted soils are often poorly understood, although both are widely studied in the context of phytostabilization. To address this issue, a novel compost-diatomite hybrid (CDH) amendment was developed and applied for assisted phytostabilization at two external temperature regimes. (Cd/Ni/Cu/Zn)-extremely polluted soils (unenriched and CDH-enriched) were cultivated with perennial ryegrass and native soil microbiome under greenhouse conditions and then transferred to freeze-thaw conditions (FTC). The decrease in metal potential toxicity in soils subjected to phytostabilization following both temperature treatments was characterized by a combination of sequential extraction and atomic absorption measurements. The soil microbiome was characterized by high-throughput sequencing. In a relative comparison, the greatest decrease in the content of all PTEs in CDH-enriched soil (compared to unenriched soil) appeared in FTC. Furthermore, under the influence of FTC, in the relative comparison between two CDH-enriched soils (exposed-, and not-exposed- to FTC) and two unenriched soils (exposed-, and not-exposed- to FTC), the content of all PTEs decreased more sharply in the CDH-enriched series than in the unenriched series. The largest redistribution into four sequentially extracted fractions in CDH-enriched soil was found for Zn. Based on the distribution pattern, Zn immobilization was greater in CDH-enriched soil in FTC. CDH increased species richness in the soil, while FTC stimulated the growth of Bacteroidia, Alphaproteobacteria, Theromomicrobia, and Gammaproteobacteria. The analysis of the functionalities of the microbiome indicated enhanced metal transportation and defense systems in samples exposed to FTC. The current research is crucial for understanding how extreme environmental conditions in both cases high pollutant levels and low temperatures affect the movement and transformation of PTEs in polluted soils during phytostabilization.
Collapse
Affiliation(s)
- Maja Radziemska
- Institute of Environmental Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Aurelia Blazejczyk
- Institute of Civil Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Mariusz Z Gusiatin
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Słoneczna St. 45G, 10-719 Olsztyn, Poland
| | - Agnieszka Cydzik-Kwiatkowska
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Słoneczna St. 45G, 10-719 Olsztyn, Poland
| | - Grzegorz Majewski
- Institute of Environmental Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Martin Brtnický
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic
| |
Collapse
|
12
|
B. Abraham S, Al-Marzooq F, Samaranayake L, Hamoudi RA, Himratul-Aznita WH, Aly Ahmed HM. Molecular analyses indicate profuse bacterial diversity in primary and post- treatment endodontic infections within a cohort from the United Arab Emirates-A preliminary study. PLoS One 2024; 19:e0305537. [PMID: 39008450 PMCID: PMC11249272 DOI: 10.1371/journal.pone.0305537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/31/2024] [Indexed: 07/17/2024] Open
Abstract
OBJECTIVE Endodontic microbiota appears to undergo evolutionary changes during disease progression from inflammation to necrosis and post-treatment. The aim of this study was to compare microbiome composition and diversity in primary and post-treatment endodontic infections from a cohort of patients from the UAE. DESIGN Intracanal samples were collected from primarily infected (n = 10) and post-treatment infected (n = 10) root canals of human teeth using sterile paper points. Bacterial DNA was amplified from seven hypervariable regions (V2-V4 and V6-V9) of the 16S rRNA gene, then sequenced using next-generation sequencing technology. The data was analyzed using appropriate bioinformatic tools. RESULTS Analyses of all the samples revealed eight major bacterial phyla, 112 genera and 260 species. Firmicutes was the most representative phylum in both groups and was significantly more abundant in the post-treatment (54.4%) than in primary (32.2%) infections (p>0.05). A total of 260 operational taxonomic units (OTUs) were identified, of which 126 (48.5%) were shared between the groups, while 83 (31.9%) and 51 (19.6%) disparate species were isolated from primary and post-treatment infections, respectively. A significant difference in beta, but not alpha diversity was noted using several different indices (p< 0.05). Differential abundance analysis indicated that, Prevotella maculosa, Streptococcus constellatus, Novosphigobium sediminicola and Anaerococcus octavius were more abundant in primary infections while Enterrococcus faecalis, Bifidobacterium dentium, Olsenella profusa and Actinomyces dentalis were more abundant in post-treatment infections (p <0.05). CONCLUSION Significant differences in the microbiome composition and diversity in primary and post-treatment endodontic infections were noted in our UAE cohort. Such compositional differences of microbiota at various stages of infection could be due to both intrinsic and extrinsic factors impacting the root canal ecosystem during disease progression, as well as during their therapeutic management. Identification of the key microbiota in primarily and secondarily infected root canals can guide in the management of these infections.
Collapse
Affiliation(s)
- Sheela B. Abraham
- Department of Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Farah Al-Marzooq
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, UAE
| | - Lakshman Samaranayake
- Faculty of Dentistry, University of Hong Kong, Hong Kong
- Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Rifat Akram Hamoudi
- Research Institute for Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Sciences, University College London, London, United Kingdom
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of Sharjah, Sharjah, United Arab Emirates
| | - Wan Harun Himratul-Aznita
- Department of Oral & Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaya
| | - Hany Mohamed Aly Ahmed
- Department of Restorative Dentistry, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaya
| |
Collapse
|
13
|
Jimenez N, Norton T, Diadala G, Bell E, Valenti M, Farland LV, Mahnert N, Herbst-Kralovetz MM. Vaginal and rectal microbiome contribute to genital inflammation in chronic pelvic pain. BMC Med 2024; 22:283. [PMID: 38972981 PMCID: PMC11229265 DOI: 10.1186/s12916-024-03500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Chronic pelvic pain (CPP) is a multifactorial syndrome that can substantially affect a patient's quality of life. Endometriosis is one cause of CPP, and alterations of the immune and microbiome profiles have been observed in patients with endometriosis. The objective of this pilot study was to investigate differences in the vaginal and gastrointestinal microbiomes and cervicovaginal immune microenvironment in patients with CPP and endometriosis diagnosis compared to those with CPP without endometriosis and no CPP. METHODS Vaginal swabs, rectal swabs, and cervicovaginal lavages (CVL) were collected among individuals undergoing gynecologic laparoscopy. Participants were grouped based on patients seeking care for chronic pain and/or pathology results: CPP and endometriosis (CPP-Endo) (n = 35), CPP without endometriosis (n = 23), or patients without CPP or endometriosis (controls) (n = 15). Sensitivity analyses were performed on CPP with endometriosis location, stage, and co-occurring gynecologic conditions (abnormal uterine bleeding, fibroids). 16S rRNA sequencing was performed to profile the microbiome, and a panel of soluble immune mediators was quantified using a multiplex assay. Statistical analysis was conducted with SAS, R, MicrobiomeAnalyst, MetaboAnalyst, and QIIME 2. RESULTS Significant differences were observed between participants with CPP alone, CPP-Endo, and surgical controls for body mass index, ethnicity, diagnosis of ovarian cysts, and diagnosis of fibroids. In rectal microbiome analysis, both CPP alone and CPP-Endo exhibited lower alpha diversity than controls, and both CPP groups revealed enrichment of irritable bowel syndrome-associated bacteria. CPP-Endo exhibited an increased abundance of vaginal Streptococcus anginosus and rectal Ruminococcus. Patients with CPP and endometrioma (s) demonstrated increased vaginal Streptococcus, Lactobacillus, and Prevotella compared to other endometriosis sites. Further, abnormal uterine bleeding was associated with an increased abundance of bacterial vaginosis-associated bacteria. Immunoproteomic profiles were distinctly clustered by CPP alone and CPP-Endo compared to controls. CPP-Endo was enriched in TNF⍺, MDC, and IL-1⍺. CONCLUSIONS Vaginal and rectal microbiomes were observed to differ between patients with CPP alone and CPP with endometriosis, which may be useful in personalized treatment for individuals with CPP and endometriosis from those with other causes of CPP. Further investigation is warranted in patients with additional co-occurring conditions, such as AUB/fibroids, which add additional complexity to these conditions and reveal the enrichment of distinct pathogenic bacteria in both mucosal sites. This study provides foundational microbiome-immunoproteomic knowledge related to chronic pelvic pain, endometriosis, and co-occurring gynecologic conditions that can help improve the treatment of patients seeking care for pain.
Collapse
Affiliation(s)
- Nicole Jimenez
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Taylor Norton
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Gurbeen Diadala
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
| | - Emerald Bell
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
- University of Arizona College of Nursing, Tucson, AZ, USA
| | - Michelle Valenti
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Leslie V Farland
- UA Cancer Center, University of Arizona, Tucson, AZ, USA
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
- Department of Obstetrics and Gynecology, College of Medicine Tucson, University of Arizona, Tucson, AZ, USA
| | - Nichole Mahnert
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Melissa M Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA.
- UA Cancer Center, University of Arizona, Tucson, AZ, USA.
| |
Collapse
|
14
|
Ezz El Deen NM, Karem M, El Borhamy MI, Hanora AMS, Fahmy N, Zakeer S. Multivariate Analysis and Correlation Study Shows the Impact of Anthropometric and Demographic Variables on Gut Microbiota in Obese Egyptian Children. Curr Microbiol 2024; 81:259. [PMID: 38972943 DOI: 10.1007/s00284-024-03771-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024]
Abstract
Deciphering the gut microbiome's link to obesity is crucial. Our study characterized the gut microbial community in Egyptian children and investigated the effect of covariates on the gut microbiome, body mass index (BMI), geographical location, gender, and age. We used 16S rRNA sequencing to characterize the gut microbial communities of 49 children. We then evaluated these communities for diversity, potential biomarkers, and functional capacity. Alpha diversity of the non-obese group was higher than that of the obese group (Chao1, P = 0.006 and observed species, P = 0.003). Beta diversity analysis revealed significant variations in the gut microbiome between the two geographical locations, Cairo and Ismailia (unweighted UniFrac, P = 0.03) and between obesity statuses, obese and non-obese (weighted UniFrac, P = 0.034; unweighted UniFrac, P = 0.015). We observed a significantly higher Firmicutes/Bacteroidetes ratio in obese males than in non-obese males (P = 0.004). Interestingly, this difference was not seen in females (P = 0.77). Multivariable association with linear models (MaAsLin2) identified 8 microbial features associated with obesity, 12 associated with non-obesity, and found 29 and 13 features specific to Cairo and Ismailia patients, respectively. It has also shown one microbial feature associated with patients under five years old. MaAsLin2, however, failed to recognize any association between gender and the gut microbiome. Moreover, it could find the most predominant features in groups 2-9 but not in group 1. Another method used in the analysis is the Linear discriminant analysis Effect Size (LEfSe) approach, which effectively identified 19 biomarkers linked to obesity, 9 linked non-obesity, 20 linked to patients residing in Cairo, 14 linked to patients in Ismailia, one linked to males, and 12 linked to females. LEfSe could not, however, detect any prevalent bacteria among children younger or older than five. Future studies should take advantage of such correlations, specifically BMI, to determine the interventions needed for obesity management.
Collapse
Affiliation(s)
- Nada Mohamed Ezz El Deen
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Mona Karem
- Department of Pediatrics, Endocrinology and Diabetes Division, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Mervat Ismail El Borhamy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Amro Mohamed Said Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, King Salman International University, Ras Sudr, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Nora Fahmy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University-Kantara Branch, Ismailia, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
15
|
Hirsch P, Molano LA, Engel A, Zentgraf J, Rahmann S, Hannig M, Müller R, Kern F, Keller A, Schmartz G. Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics. Nucleic Acids Res 2024; 52:W407-W414. [PMID: 38716863 PMCID: PMC11223814 DOI: 10.1093/nar/gkae364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 07/06/2024] Open
Abstract
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the analysis of large sequencing data and are now widely used to annotate metagenomic data. We make use of k-mer counting techniques for efficient and accurate compositional analysis of microbiota from whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual preprocessing or complete data exchange. It handles diverse sequencing platforms, including short single-end, paired-end, and long read technologies. Our sketch-based workflow significantly reduces the data volume transferred from the user to the server (up to 99.59% size reduction) to subsequently perform taxonomic profiling with enhanced efficiency and privacy. Mibianto offers functionality beyond k-mer quantification; it supports advanced community composition estimation, including diversity, ordination, and differential abundance analysis. Our tool aids in the standardization of computational workflows, thus supporting reproducibility of scientific sequencing studies. It is adaptable to small- and large-scale experimental designs and offers a user-friendly interface, thus making it an invaluable tool for both clinical and research-oriented metagenomic studies. Mibianto is freely available without the need for a login at: https://www.ccb.uni-saarland.de/mibianto.
Collapse
Affiliation(s)
- Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jens Zentgraf
- Algorithmic Bioinformatics, Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Sven Rahmann
- Algorithmic Bioinformatics, Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Hospital, Saarland University, Kirrberger Str. 100, Building 73, 66421 Homburg, Saar, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, 38124 Braunschweig, Germany
- PharmaScienceHub, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
- PharmaScienceHub, 66123 Saarbrücken, Germany
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| |
Collapse
|
16
|
Brar NK, Dhariwal A, Shekhar S, Junges R, Hakansson AP, Petersen FC. HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome. Front Microbiol 2024; 15:1406190. [PMID: 39101559 PMCID: PMC11254628 DOI: 10.3389/fmicb.2024.1406190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.
Collapse
Affiliation(s)
- Navdeep Kaur Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Sudhanshu Shekhar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Anders P. Hakansson
- Institute of Experimental Infection Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | | |
Collapse
|
17
|
Shukla R, Tsuchiya Y, Behari A, Ikoma T, Nakamura K, Kapoor VK. Metagenomic Analysis of Biliary Microbial Flora in Patients with Gallbladder Cancer or Gallstones-Associated Chronic Cholecystitis. Cancer Invest 2024; 42:478-490. [PMID: 38845533 DOI: 10.1080/07357907.2024.2361305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/25/2024] [Indexed: 07/13/2024]
Abstract
Biliary dysbiosis is associated with gallbladder cancer (GBC). We aimed to look for biliary bacteria specifically detected in GBC patients. We used 16S rRNA-based metagenomic analysis to elucidate biliary microbiota in 30 GBC and 30 gallstones-associated chronic cholecystitis patients. Relative abundance of five genera, Streptococcus, Enterococcus, Halomonas, Escherichia and Caulobacter was significantly associated with GBC. Of 15-species, 7 were detected significantly higher in GBC, Streptococcus anginosus, Streptococcus constellatus, Streptococcus intermedius, Actinomyces bowdenii, Actinomyces israelii, Actinomyces gerencseriae, and Escherichia fergusonii were biosafety level-2 infectious bacteria; other 8 species were biosafety level-1 bacteria. These bacterial species may be involved in pathogenesis of GBC.
Collapse
Affiliation(s)
- Ratnakar Shukla
- Department of Clinical Research, Sharda School of Allied Health Sciences, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Yasuo Tsuchiya
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Anu Behari
- Department of Surgical Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Toshikazu Ikoma
- Department of Clinical Laboratory, Uji-Tokushukai Medical Center, Uji, Japan
| | - Kazutoshi Nakamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Vinay K Kapoor
- Department of Hepato-pancreato-biliary (HPB) Surgery, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
| |
Collapse
|
18
|
Vieira WDA, de-Jesus-Soares A, Lopes EM, Gomes BPFA, Lima BP. Effect of supplementary sodium hypochlorite agitation techniques on an ex vivo oral multispecies biofilm during passive disinfection of simulated immature roots. Int Endod J 2024; 57:966-980. [PMID: 38387884 DOI: 10.1111/iej.14053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 02/24/2024]
Abstract
AIM To compare the effect of different sodium hypochlorite (NaOCl) agitation techniques on an ex vivo oral multispecies biofilm during passive disinfection of simulated immature roots. METHODOLOGY Extracted human teeth were prepared to simulate immature roots. They were infected with a dental plaque-derived multispecies biofilm and cultured for 14 days. The roots were randomly designated into four groups: (1) negative control (PBS), (2) 1.5% NaOCl (CNI), (3) CNI + Ultrasonic activation (UA), (4) CNI + EasyClean agitation (ECA), (5) CNI + XP-endo finisher agitation (XPF), and (6) positive control (6% NaOCl). Biofilm samples were collected from the root canals and used to determine the number of viable cells (colony-forming units), scanning electron microscopy, and 16S rRNA gene sequencing. The mean colony-forming units per mL (CFU/mL) were analysed using One-way anova. 16S rRNA sequencing data were analysed for alpha (observed OTUs, Shannon index, and Chao1) and beta diversity (Bray-Curtis dissimilarities). The LEfSe analysis was used to determine the effect of treatment procedures on the abundance of root canal microbiota. The significance was set at .05. RESULTS PBS and CNI samples had significantly higher CFU/mL counts than UA, ECA, XPF, and 6% NaOCl samples (p < .05). The pre-treatment, PBS, and CNI groups had significantly greater alpha diversity than the UA, ECA, XPF, and 6% NaOCl groups (p < .05). NaOCl agitation groups and the 6% NaOCl group achieved a more pronounced reduction in bacteria from the genera Fusobacterium, Actinomyces, Porphyromonas, and Capnocytophaga. CONCLUSIONS The effectiveness of passive disinfection protocols was enhanced by NaOCl agitation techniques, suggesting that this supplementary method can improve the outcome of revitalization procedures.
Collapse
Affiliation(s)
- Walbert de Andrade Vieira
- Division of Endodontics, Department of Restorative Dentistry, Piracicaba Dental School, Universidade Estadual de Campinas - UNICAMP, Piracicaba, Brazil
| | - Adriana de-Jesus-Soares
- Division of Endodontics, Department of Restorative Dentistry, Piracicaba Dental School, Universidade Estadual de Campinas - UNICAMP, Piracicaba, Brazil
| | - Erica M Lopes
- Division of Endodontics, Department of Restorative Dentistry, Piracicaba Dental School, Universidade Estadual de Campinas - UNICAMP, Piracicaba, Brazil
| | - Brenda P F A Gomes
- Division of Endodontics, Department of Restorative Dentistry, Piracicaba Dental School, Universidade Estadual de Campinas - UNICAMP, Piracicaba, Brazil
| | - Bruno P Lima
- Division of Basic Sciences, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
19
|
Muralidharan J, Ruiz-Limón P, Gomez-Perez AM, Murri M, Vioque J, Corella D, Fitó M, Vidal J, Salas-Salvadó J, Torres-Collado L, Coltell O, Atzeni A, Castañer O, Bulló M, Bernal-López MR, Moreno-Indias I, Tinahones FJ. Physical activity shifts gut microbiota structure in aged subjects with overweight/obesity and metabolic syndrome. Biol Sport 2024; 41:47-60. [PMID: 38952913 PMCID: PMC11167471 DOI: 10.5114/biolsport.2024.133005] [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: 08/10/2023] [Revised: 08/25/2023] [Accepted: 10/22/2023] [Indexed: 07/03/2024] Open
Abstract
We aimed to identify how physical activity (PA), within the context of a Mediterranean diet, affects metabolic variables and gut microbiota in older individuals with overweight/obesity and metabolic syndrome. Observational analysis was conducted as part of the PREDIMED-Plus study with 152 males and 145 females with overweight/obesity and metabolic syndrome. General assessments, anthropometric and biochemical measurements, and gut microbial 16S rRNA sequencing data were analyzed at baseline and 1-year of follow-up. Participants were stratified by tertiles of 1-year change in total PA-related energy expenditure ranging from -98.77 to 1099.99 METs (min/week). The total PA percentage of change was reduced in tertile 1 (-44.83 ± 24.94), increased in tertile 2 (28.96 ± 23.33) and tertile 3 (273.64 ± 221.42). Beta diversity analysis showed differences in the gut microbiota population within each tertile group. Significant differences were found at phylum, family, and genus levels in the gut microbiota of the three tertile groups at baseline and 1-year timepoint. Tertile 3, the group with the greatest increase in PA, was characterized by increases in their levels of Sutterella, Bilophila, and Lachnospira bacteria as well as a reduction in Collinsella. Moreover, this tertile showed a different pattern in its predicted metabolic capacities to the other groups. Our results have demonstrated that changes in PA such as lifestyle and Mediterranean diet induces specific variations in the gut microbiota profile. This modulation of gut microbiome populations and their metabolic capacities may contribute to the health of the aged individuals with overweight/obesity and metabolic syndrome.
Collapse
Affiliation(s)
- Jananee Muralidharan
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- University of Rovira i Virgili, Department of Biochemistry and Biotechnology, Human Nutrition Unit, 43003 Reus, Spain
| | - Patricia Ruiz-Limón
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, The Biomedical Research Institute of Malaga and Platform in Nanomedicine (IBIMA BIONAND Platform), University of Malaga, 29016 Malaga, Spain
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
| | - Ana M. Gomez-Perez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, The Biomedical Research Institute of Malaga and Platform in Nanomedicine (IBIMA BIONAND Platform), University of Malaga, 29016 Malaga, Spain
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
| | - Mora Murri
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, The Biomedical Research Institute of Malaga and Platform in Nanomedicine (IBIMA BIONAND Platform), University of Malaga, 29016 Malaga, Spain
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
| | - Jesús Vioque
- Institute of Health and Biomedical Research of Alicante. University of Miguel Hernández (ISABIAL-UMH), 03010 Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, 28029 Madrid, Spain
| | - Dolores Corella
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- Department of Preventive Medicine, University of Valencia, 46100 Valencia, Spain
| | - Montse Fitó
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- Cardiovascular Risk and Nutrition (Regicor Study Group), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Josep Vidal
- Endocrinology and Nutrition Department, Clinic Universitary Hospital, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Jordi Salas-Salvadó
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- University of Rovira i Virgili, Department of Biochemistry and Biotechnology, Human Nutrition Unit, 43003 Reus, Spain
- Pere i Virgili Health Research Institute (IISPV). San Joan University Hospital, 43003 Reus, Spain
| | - Laura Torres-Collado
- Institute of Health and Biomedical Research of Alicante. University of Miguel Hernández (ISABIAL-UMH), 03010 Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, 28029 Madrid, Spain
| | - Oscar Coltell
- Department of Computer Sciences. University Jaume I, Castellon, Spain
| | - Alessandro Atzeni
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- University of Rovira i Virgili, Department of Biochemistry and Biotechnology, Human Nutrition Unit, 43003 Reus, Spain
| | - Olga Castañer
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- Cardiovascular Risk and Nutrition (Regicor Study Group), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Mònica Bulló
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- University of Rovira i Virgili, Department of Biochemistry and Biotechnology, Human Nutrition Unit, 43003 Reus, Spain
| | - M. Rosa Bernal-López
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
- Department of Internal Medicine of Regional University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29009 Málaga, Spain
| | - Isabel Moreno-Indias
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, The Biomedical Research Institute of Malaga and Platform in Nanomedicine (IBIMA BIONAND Platform), University of Malaga, 29016 Malaga, Spain
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
| | - Francisco J. Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, The Biomedical Research Institute of Malaga and Platform in Nanomedicine (IBIMA BIONAND Platform), University of Malaga, 29016 Malaga, Spain
- CIBER in Physiopathology of Obesity and Nutrition (CIBEROBN), Carlos III Health Institute, 28029 Madrid, Spain
| |
Collapse
|
20
|
Lennon S, Lackie T, Miltko A, Kearns ZC, Paquette MR, Bloomer RJ, Wang A, van der Merwe M. Safety and efficacy of a probiotic cocktail containing P. acidilactici and L. plantarum for gastrointestinal discomfort in endurance runners: randomized double-blinded crossover clinical trial. Appl Physiol Nutr Metab 2024; 49:890-903. [PMID: 38427981 DOI: 10.1139/apnm-2023-0449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Probiotics are increasingly used to treat conditions associated with gastrointestinal injury and permeability, including exercise-induced gastrointestinal discomfort. This study assessed safety and efficacy of a probiotic in altering the intestinal milieu and mitigating gastrointestinal symptoms (GIS) in endurance runners. In a double blind, crossover study, 16 runners were randomized to 4 weeks of daily supplementation with a probiotic cocktail containing Pediococcus acidilactici bacteria and Lactobacillus plantarum or placebo. Fasting blood and stool samples were collected for measurement of gut permeability markers, immune parameters, and microbiome analyses. Treadmill run tests were performed before and after treatment; participants ran at 65%-70% of VO2max at 27 °C for a maximum of 90 min or until fatigue/GIS developed. A blood sample was collected after the treadmill run test. In healthy individuals, 4 weeks of probiotic supplementation did not alter health parameters, although a marginal reduction in aspartate aminotransferase levels was observed with probiotic treatment only (p = 0.05). GIS, gut permeability-associated parameters (intestinal fatty acid binding protein, lipopolysaccharide binding protein, zonulin, and cytokines), and intestinal microbial content were not altered by the probiotic supplementation. Post-run measurements of GIS and gut-associated parameters did not differ between groups; however, the observed lack of differences is confounded by an absence of measurable functional outcome as GIS was not sufficiently induced during the run. Under the current study conditions, the probiotic was safe to use, and did not affect gut- or immune-associated parameters, or intestinal symptoms in a healthy population. The probiotic might reduce tissue damage, but more studies are warranted.
Collapse
Affiliation(s)
- Sarah Lennon
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Thomas Lackie
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Adriana Miltko
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Zoey C Kearns
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Maxime R Paquette
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Richard J Bloomer
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Anyou Wang
- Harry Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152, USA
| | - Marie van der Merwe
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| |
Collapse
|
21
|
Jiang Q, Sherlock DN, Elolimy AA, Yoon I, Loor JJ. Feeding a Saccharomyces cerevisiae fermentation product during a gut barrier challenge in lactating Holstein cows impacts the ruminal microbiota and metabolome. J Dairy Sci 2024; 107:4476-4494. [PMID: 38369118 DOI: 10.3168/jds.2023-24147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Through its influence on the gut microbiota, the feeding of Saccharomyces cerevisiae fermentation products (SCFP) has been a successful strategy to enhance the health of dairy cows during periods of physiological stresses. Although production and metabolic outcomes from feeding SCFP are well-known, its combined impacts on the ruminal microbiota and metabolome during gut barrier challenges remain unclear. To address this gap in knowledge, multiparous Holstein cows (97.1 ± 7.6 DIM [SD]; n = 8/group) fed a control diet (CON) or CON plus 19 g/d SCFP for 9 wk were subjected to a feed restriction (FR) challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before FR. The DNA extracted from ruminal fluid was subjected to PacBio full-length 16S rRNA gene sequencing, real-time PCR of 12 major ruminal bacteria, and metabolomics analysis of up to 189 metabolites via GC/MS. High-quality amplicon sequence analyses were performed with the TADA (Targeted Amplicon Diversity Analysis), MicrobiomeAnalyst, PICRUSt2, and STAMP software packages, and metabolomics data were analyzed via MetaboAnalyst 5.0. Ruminal fluid metabolites from the SCFP group exhibited a greater α-diversity Chao 1 (P = 0.03) and Shannon indices (P = 0.05), and the partial least squares discriminant analysis clearly discriminated metabolite profiles between dietary groups. The abundance of CPla_4_termite_group, Candidatus Saccharimonas, Oribacterium, and Pirellula genus in cows fed SCFP was greater. In the SCFP group, concentrations of ethanolamine, 2-amino-4,6-dihydroxypyrimidine, glyoxylic acid, serine, threonine, cytosine, stearic acid, and pyrrole-2-carboxylic acid were greater in ruminal fluid. Both Fretibacterium and Succinivibrio abundances were positively correlated with metabolites across various biological processes: gamma-aminobutyric acid, galactose, butane-2,3-diol, fructose, 5-amino pentanoic acid, β-aminoisobutyric acid, ornithine, malonic acid, 3-hydroxy-3-methylbutyric acid, hexanoic acid, heptanoic acid, cadaverine, glycolic acid, β-alanine, 2-hydroxybutyric acid, methyl alanine, and alanine. In the SCFP group, compared with CON, the mean proportion of 14 predicted pathways based on metabolomics data was greater, whereas 10 predicted pathways were lower. Integrating metabolites and upregulated predicted enzymes (NADP+-dependent glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, serine: glyoxylate aminotransferase, and d-glycerate 3-kinase) indicated that the pentose phosphate pathway and photorespiration pathway were most upregulated by SCFP. Overall, SCFP during FR led to alterations in ruminal microbiota composition and key metabolic pathways. Among those, we identified a shift from the tricarboxylic acid cycle to the glyoxylate cycle, and nitrogenous base production was enhanced.
Collapse
Affiliation(s)
- Qianming Jiang
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801
| | | | - Ahmed A Elolimy
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801; Livestock Production and Management, Department of Integrated Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 1551, United Arab Emirates
| | | | - Juan J Loor
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801.
| |
Collapse
|
22
|
Idowu AP, Yamamoto K, Koizumi T, Matsutani M, Takada K, Shiwa Y, Asfaw A, Matsumoto R, Ouyabe M, Pachakkil B, Kikuno H, Shiwachi H. Changes in the rhizosphere and root-associated bacteria community of white Guinea yam ( Dioscorea rotundata Poir.) impacted by genotype and nitrogen fertilization. Heliyon 2024; 10:e33169. [PMID: 39021943 PMCID: PMC11252748 DOI: 10.1016/j.heliyon.2024.e33169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
The bacterial diversity and composition of water yam (Dioscorea alata L. cv. A-19), which can grow without chemical fertilization, have recently been characterized with no significant differences compared with the use of chemical fertilization. However, the diversity and community structure of bacteria associated with the white Guinea yam (Dioscorea rotundata), the most cultivated and economically important yam in West Africa, have not yet been investigated. This study characterized the bacterial diversity and composition associated with bulk soil, rhizosphere, and plant roots in six white Guinea yam genotypes (S004, S020, S032, S042, S058, and S074) in field experiments in Ibadan, Nigeria under N-based chemical fertilizer application. The largest diversity of bacteria was found in the bulk soil, followed by the rhizosphere and roots. Based on the alpha diversity analysis, the bacterial diversity in both S020 and S042 increased with fertilizer application among the bulk soil samples. S058 grown under no-fertilizer conditions had the highest bacterial diversity among the rhizosphere samples. Beta diversity analysis highlighted the significant difference in the composition of bacteria associated with the genotypes and fertilizer treatments, and S032 had a unique bacterial composition compared to the other genotypes. The dominant phylum across all sample types was Proteobacteria. Actinobacteriota was the dominant phylum among bulk soil samples. At the genus level, Bacillus was the most abundant bacterial genus across both the control and treated samples. Pseudomonas was predominant across all rhizosphere samples. Chryseobacterium, Sphingobium, Delftia and Klebsiella associated with the rhizosphere were shown the altered relative abundance between the control and treated samples depending on genotypes. A genus related to symbiotic nitrogen-fixing bacteria, the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, showed higher relative abundance among all root samples, indicating that it is a core bacterial genus. Furthermore, the field application of chemical fertilizer had a significant impact on the relative abundances of two genera related to symbiotic nitrogen-fixers, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade and Bradyrhizobium in the rhizosphere and root. These results suggest that N-based chemical fertilizers and plant genotypes would influence the compositional arrangement of associated bacterial communities, including symbiotic nitrogen-fixing bacteria.
Collapse
Affiliation(s)
- Ayodeji Peter Idowu
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Takahiko Koizumi
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Kanako Takada
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), PMB 5320 Oyo Road Ibadan, Nigeria
| | - Ryo Matsumoto
- International Institute of Tropical Agriculture (IITA), PMB 5320 Oyo Road Ibadan, Nigeria
| | - Michel Ouyabe
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Babil Pachakkil
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Hidehiko Kikuno
- Miyako Subtropical Training and Research Farm, Tokyo University of Agriculture, Okinawa, Japan
| | - Hironobu Shiwachi
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| |
Collapse
|
23
|
Onyango MG, Payne AF, Stout J, Dieme C, Kuo L, Kramer LD, Ciota AT. Aedes albopictus saliva contains a richer microbial community than the midgut. Parasit Vectors 2024; 17:267. [PMID: 38918848 PMCID: PMC11197185 DOI: 10.1186/s13071-024-06334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Past findings demonstrate that arthropods can egest midgut microbiota into the host skin leading to dual colonization of the vertebrate host with pathogens and saliva microbiome. A knowledge gap exists on how the saliva microbiome interacts with the pathogen in the saliva. To fill this gap, we need to first define the microbial composition of mosquito saliva. METHODS The current study aimed at analyzing and comparing the microbial profile of Aedes albopictus saliva and midgut as well as assessing the impact of Zika virus (ZIKV) infection on the midgut and saliva microbial composition. Colony-reared Ae. albopictus strains were either exposed to ZIKV infectious or noninfectious bloodmeal. At 14 ays postinfection, the 16S V3-V4 hypervariable rRNA region was amplified from midgut and saliva samples and sequenced on an Illumina MiSeq platform. The relative abundance and diversity of midgut and saliva microbial taxa were assessed. RESULTS We observed a richer microbial community in the saliva compared with the midgut, yet some of the microbial taxa were common in the midgut and saliva. ZIKV infection did not impact the microbial diversity of midgut or saliva. Further, we identified Elizabethkingia spp. in the Ae. albopictus saliva. CONCLUSIONS This study provides insights into the microbial community of the Ae. albopictus saliva as well as the influence of ZIKV infection on the microbial composition of its midgut and saliva. The identification of Elizabethkingia spp., an emerging pathogen of global health significance, in Ae. albopictus saliva is of medical importance. Future studies to assess the interactions between Ae. albopictus saliva microbiome and ZIKV could lead to novel strategies for developing transmission barrier tools.
Collapse
Affiliation(s)
- Maria G Onyango
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, Texas, 79409-3131, USA.
| | - Anne F Payne
- New York State Department of Health, Wadsworth Center, 5668 State Farm Road, Slingerlands, NY, 12159, USA
| | - Jessica Stout
- New York State Department of Health, Wadsworth Center, 5668 State Farm Road, Slingerlands, NY, 12159, USA
| | - Constentin Dieme
- New York State Department of Health, Wadsworth Center, 5668 State Farm Road, Slingerlands, NY, 12159, USA
| | - Lili Kuo
- New York State Department of Health, Wadsworth Center, 5668 State Farm Road, Slingerlands, NY, 12159, USA
| | - Laura D Kramer
- School of Public Health, State University of New York Albany, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Alexander T Ciota
- New York State Department of Health, Wadsworth Center, 5668 State Farm Road, Slingerlands, NY, 12159, USA
- School of Public Health, State University of New York Albany, 1400 Washington Avenue, Albany, NY, 12222, USA
| |
Collapse
|
24
|
Iqbal A, Hussain Q, Mo Z, Hua T, Mustafa AEZMA, Tang X. Vermicompost Supply Enhances Fragrant-Rice Yield by Improving Soil Fertility and Eukaryotic Microbial Community Composition under Environmental Stress Conditions. Microorganisms 2024; 12:1252. [PMID: 38930634 PMCID: PMC11206116 DOI: 10.3390/microorganisms12061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Heavy-metal contamination in agricultural soil, particularly of cadmium (Cd), poses serious threats to soil biodiversity, rice production, and food safety. Soil microbes improve soil fertility by regulating soil organic matter production, plant nutrient accumulation, and pollutant transformation. Addressing the impact of Cd toxicity on soil fungal community composition, soil health, and rice yield is urgently required for sustainable rice production. Vermicompost (VC) is an organic fertilizer that alleviates the toxic effects of Cd on soil microbial biodiversity and functionality and improves crop productivity sustainably. In the present study, we examined the effects of different doses of VC (i.e., 0, 3, and 6 tons ha-1) and levels of Cd stress (i.e., 0 and 25 mg Cd kg-1) on soil biochemical attributes, soil fungal community composition, and fragrant-rice grain yield. The results showed that the Cd toxicity significantly reduced soil fertility, eukaryotic microbial community composition and rice grain yield. However, the VC addition alleviated the Cd toxicity and significantly improved the soil fungal community; additionally, it enhanced the relative abundance of Ascomycota, Chlorophyta, Ciliophora, Basidiomycota, and Glomeromycta in Cd-contaminated soils. Moreover, the VC addition enhanced the soil's chemical attributes, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), and microbial biomass C and N, compared to non-VC treated soil under Cd toxicity conditions. Similarly, the VC application significantly increased rice grain yield and decreased the Cd uptake in rice. One possible explanation for the reduced Cd uptake in plants is that VC amendments influence the soil's biological properties, which ultimately reduces soil Cd bioavailability and subsequently influences the Cd uptake and accumulation in rice plants. RDA analysis determined that the leading fungal species were highly related to soil environmental attributes and microbial biomass C and N production. However, the relative abundance levels of Ascomycota, Basidiomycota, and Glomeromycta were strongly associated with soil environmental variables. Thus, the outcomes of this study reveal that the use of VC in Cd-contaminated soils could be useful for sustainable rice production and safe utilization of Cd-polluted soil.
Collapse
Affiliation(s)
- Anas Iqbal
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (A.I.)
- Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Quaid Hussain
- College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Zhaowen Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (A.I.)
- Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Tian Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (A.I.)
- Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| | - Abd El-Zaher M. A. Mustafa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh P.O. Box 11451, Saudi Arabia;
| | - Xiangru Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (A.I.)
- Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China
| |
Collapse
|
25
|
Kochumon S, Malik MZ, Sindhu S, Arefanian H, Jacob T, Bahman F, Nizam R, Hasan A, Thomas R, Al-Rashed F, Shenouda S, Wilson A, Albeloushi S, Almansour N, Alhamar G, Al Madhoun A, Alzaid F, Thanaraj TA, Koistinen HA, Tuomilehto J, Al-Mulla F, Ahmad R. Gut Dysbiosis Shaped by Cocoa Butter-Based Sucrose-Free HFD Leads to Steatohepatitis, and Insulin Resistance in Mice. Nutrients 2024; 16:1929. [PMID: 38931284 PMCID: PMC11207001 DOI: 10.3390/nu16121929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND High-fat diets cause gut dysbiosis and promote triglyceride accumulation, obesity, gut permeability changes, inflammation, and insulin resistance. Both cocoa butter and fish oil are considered to be a part of healthy diets. However, their differential effects on gut microbiome perturbations in mice fed high concentrations of these fats, in the absence of sucrose, remains to be elucidated. The aim of the study was to test whether the sucrose-free cocoa butter-based high-fat diet (C-HFD) feeding in mice leads to gut dysbiosis that associates with a pathologic phenotype marked by hepatic steatosis, low-grade inflammation, perturbed glucose homeostasis, and insulin resistance, compared with control mice fed the fish oil based high-fat diet (F-HFD). RESULTS C57BL/6 mice (5-6 mice/group) were fed two types of high fat diets (C-HFD and F-HFD) for 24 weeks. No significant difference was found in the liver weight or total body weight between the two groups. The 16S rRNA sequencing of gut bacterial samples displayed gut dysbiosis in C-HFD group, with differentially-altered microbial diversity or relative abundances. Bacteroidetes, Firmicutes, and Proteobacteria were highly abundant in C-HFD group, while the Verrucomicrobia, Saccharibacteria (TM7), Actinobacteria, and Tenericutes were more abundant in F-HFD group. Other taxa in C-HFD group included the Bacteroides, Odoribacter, Sutterella, Firmicutes bacterium (AF12), Anaeroplasma, Roseburia, and Parabacteroides distasonis. An increased Firmicutes/Bacteroidetes (F/B) ratio in C-HFD group, compared with F-HFD group, indicated the gut dysbiosis. These gut bacterial changes in C-HFD group had predicted associations with fatty liver disease and with lipogenic, inflammatory, glucose metabolic, and insulin signaling pathways. Consistent with its microbiome shift, the C-HFD group showed hepatic inflammation and steatosis, high fasting blood glucose, insulin resistance, increased hepatic de novo lipogenesis (Acetyl CoA carboxylases 1 (Acaca), Fatty acid synthase (Fasn), Stearoyl-CoA desaturase-1 (Scd1), Elongation of long-chain fatty acids family member 6 (Elovl6), Peroxisome proliferator-activated receptor-gamma (Pparg) and cholesterol synthesis (β-(hydroxy β-methylglutaryl-CoA reductase (Hmgcr). Non-significant differences were observed regarding fatty acid uptake (Cluster of differentiation 36 (CD36), Fatty acid binding protein-1 (Fabp1) and efflux (ATP-binding cassette G1 (Abcg1), Microsomal TG transfer protein (Mttp) in C-HFD group, compared with F-HFD group. The C-HFD group also displayed increased gene expression of inflammatory markers including Tumor necrosis factor alpha (Tnfa), C-C motif chemokine ligand 2 (Ccl2), and Interleukin-12 (Il12), as well as a tendency for liver fibrosis. CONCLUSION These findings suggest that the sucrose-free C-HFD feeding in mice induces gut dysbiosis which associates with liver inflammation, steatosis, glucose intolerance and insulin resistance.
Collapse
Affiliation(s)
- Shihab Kochumon
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Md. Zubbair Malik
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Sardar Sindhu
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Hossein Arefanian
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Texy Jacob
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Fatemah Bahman
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Rasheeba Nizam
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Amal Hasan
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Reeby Thomas
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Fatema Al-Rashed
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Steve Shenouda
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Ajit Wilson
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Shaima Albeloushi
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Nourah Almansour
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Ghadeer Alhamar
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Ashraf Al Madhoun
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Fawaz Alzaid
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Thangavel Alphonse Thanaraj
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Heikki A. Koistinen
- Department of Medicine, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland;
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, P.O. Box 30, 00271 Helsinki, Finland;
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, P.O. Box 30, 00271 Helsinki, Finland;
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
| | - Fahd Al-Mulla
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| | - Rasheed Ahmad
- Dasman Diabetes Institute, Dasman 15462, Kuwait; (S.K.); (M.Z.M.); (S.S.); (H.A.); (T.J.); (F.B.); (R.N.); (A.H.); (R.T.); (F.A.-R.); (S.S.); (A.W.); (S.A.); (N.A.); (G.A.); (A.A.M.); (F.A.); (T.A.T.); (F.A.-M.)
| |
Collapse
|
26
|
Arango RA, Bishell AB, Ohno KM, Shelton TG, Schoville SD, Carlos-Shanley C. Seasonal shifts in gut microbiota and cold tolerance metrics in a northern population of Reticulitermes flavipes (Blattodea: Rhinotermitidae). ENVIRONMENTAL ENTOMOLOGY 2024; 53:447-456. [PMID: 38574195 DOI: 10.1093/ee/nvae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/24/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
Eastern subterranean termites, Reticulitermes flavipes (Kollar), are widely distributed across North America where they are exposed to a broad range of environmental conditions. However, mechanisms for overwintering are not well understood. Wisconsin is a unique location to study mechanisms of cold tolerance as it represents the northern boundary for persistent R. flavipes populations. In this study, we evaluated seasonal shifts in cold tolerance using critical thermal minimum (CTmin) and supercooling point (SCP) and examined how these measurements correlate to changes in the microbial community of the termite gut. Results showed seasonal acclimatization to cold, which is consistent with the use of behavioral freeze-avoidant mechanisms. However, these insects also demonstrated an increased susceptibility to freezing later in the season, which may be tied to changes in gut microbiota. Our results found shifts in the composition of the gut microbiome in R. flavipes between mid- to late summer and early to late fall. These differences may be suggestive of a change in metabolism to adjust to a period of reduced feeding and increased metabolic stress during overwintering. Specifically, results showed an increased abundance of Methanobrevibacter sp. (Euryarchaeota) associated with cold, which may be indicative of a metabolic shift from acetogenesis to methanogenesis associated with overwintering. Further work is needed focusing on specific contributions of certain gut microbes, particularly their role in metabolic adaptability and in providing protection from oxidative stress associated with changes in environmental conditions.
Collapse
Affiliation(s)
- Rachel A Arango
- USDA Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, USA
| | - Amy B Bishell
- USDA Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, USA
| | - Katie M Ohno
- USDA Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, USA
| | - Thomas G Shelton
- USDA Forest Products Laboratory, 201 Lincoln Green, Starkville, MS, USA
| | - Sean D Schoville
- Department of Entomology, UW-Madison, 1630 Linden Drive, 637 Russell Laboratory, Madison, WI, USA
| | - Camila Carlos-Shanley
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, USA
| |
Collapse
|
27
|
Schäfer L, Grundmann SM, Rühl M, Zorn H, Seel W, Simon MC, Schuchardt S, Most E, Ringseis R, Eder K. Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers. Poult Sci 2024; 103:103975. [PMID: 38945001 PMCID: PMC11261454 DOI: 10.1016/j.psj.2024.103975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024] Open
Abstract
Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. 72 males, 1-day-old Cobb 500 broilers were randomly assigned to 3 different groups and fed 3 different adequate diets containing either 0% (PSA-0), 2.5% (PSA-2.5) and 5% (PSA-5.0) P. sapidus mycelium in a 3-phase feeding system for 35 d. Each group consisted of 6 cages (replicates) with 4 broilers/cage. Body weight gain, feed intake and feed:gain ratio and apparent ileal digestibility of crude protein, ether extract and amino acids were not different between groups. Metagenomic analysis of the cecal microbiota revealed no differences between groups, except that one α-diversity metric (Shannon index) and the abundance of 2 low-abundance bacterial taxa (Clostridia UCG 014, Eubacteriales) differed between groups (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta and concentrations of plasma lipopolysaccharide and mRNA levels of proinflammatory genes, tight-junction proteins, and mucins in the cecum mucosa did not differ between groups. None of the plasma metabolites analyzed using targeted-metabolomics differed across the groups. Hepatic transcript profiling revealed a total of 144 transcripts to be differentially expressed between group PSA-5.0 and group PSA-0 but none of these genes was regulated greater 2-fold. Considering either the lack of effects or the very weak effects of feeding the P. sapidus mycelium in the broilers it can be concluded that inclusion of a sustainably produced fungal mycelium in broiler diets at the expense of other feed components has no negative consequences on broilers´ performance and metabolism.
Collapse
Affiliation(s)
- Lea Schäfer
- Institute of Animal Nutrition and Nutrition Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - Sarah M Grundmann
- Institute of Animal Nutrition and Nutrition Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Waldemar Seel
- University of Bonn, Nutrition and Microbiota, Institute of Nutrition and Food Sciences, Bonn, Germany
| | - Marie-Christine Simon
- University of Bonn, Nutrition and Microbiota, Institute of Nutrition and Food Sciences, Bonn, Germany
| | - Sven Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Hannover, Germany
| | - Erika Most
- Institute of Animal Nutrition and Nutrition Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - Robert Ringseis
- Institute of Animal Nutrition and Nutrition Physiology, Justus Liebig University Giessen, Giessen, Germany; Center for Sustainable Food Systems, Justus Liebig University Giessen, Giessen, Germany
| | - Klaus Eder
- Institute of Animal Nutrition and Nutrition Physiology, Justus Liebig University Giessen, Giessen, Germany; Center for Sustainable Food Systems, Justus Liebig University Giessen, Giessen, Germany.
| |
Collapse
|
28
|
Piacentino D, Vizioli C, Barb JJ, Grant-Beurmann S, Bouhlal S, Battista JT, Jennings O, Lee MR, Schwandt ML, Walter P, Henderson WA, Chen K, Turner S, Yang S, Fraser CM, Farinelli LA, Farokhnia M, Leggio L. Gut microbial diversity and functional characterization in people with alcohol use disorder: A case-control study. PLoS One 2024; 19:e0302195. [PMID: 38865325 PMCID: PMC11168635 DOI: 10.1371/journal.pone.0302195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/30/2024] [Indexed: 06/14/2024] Open
Abstract
Individuals with Alcohol Use Disorder (AUD) typically have comorbid chronic health conditions, including anxiety and depression disorders, increased sleep disruption, and poor nutrition status, along with gut microbial dysbiosis. To better understand the effects of gut dysbiosis previously shown in individuals with AUD, gut microbiome and metabolome were investigated between three cohorts. Two groups of individuals with AUD included treatment-seeking newly abstinent for at least six weeks (AB: N = 10) and non-treatment-seeking currently drinking (CD: N = 9) individuals. The third group was age, gender, and BMI-matched healthy controls (HC: N = 12). Deep phenotyping during two weeks of outpatient National Institutes of Health Clinical Center visits was performed, including clinical, psychological, medical, metabolic, dietary, and experimental assessments. Alpha and beta diversity and differential microbial taxa and metabolite abundance of the gut microbiome were examined across the three groups. Metabolites derived from the lipid super-pathway were identified to be more abundant in the AB group compared to CD and HC groups. The AB individuals appeared to be most clinically different from CD and HC individuals with respect to their gut microbiome and metabolome. These findings highlight the potential long-term effects of chronic alcohol use in individuals with AUD, even during short-term abstinence.
Collapse
Affiliation(s)
- Daria Piacentino
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Carlotta Vizioli
- Interoceptive Disorders Unit, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, United States of America
| | - Jennifer J. Barb
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, NIH, Bethesda, MD, United States of America
| | - Silvia Grant-Beurmann
- Institute for Genome Sciences and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Sofia Bouhlal
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Jillian T. Battista
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Olivia Jennings
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Mary R. Lee
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Melanie L. Schwandt
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Bethesda, MD, United States of America
| | - Peter Walter
- National Institute of Diabetes and Digestive and Kidney Diseases Division of Intramural Research, NIH, Bethesda, MD, United States of America
| | - Wendy A. Henderson
- Department of Biobehavioral Health Sciences, University of Pennsylvania School of Nursing, Philadelphia, PA, United States of America
| | - Kun Chen
- Department of Statistics, University of Connecticut, Storrs, CT, United States of America
| | - Sara Turner
- Nutrition Department, Clinical Center, NIH, Bethesda, MD, United States of America
| | - Shanna Yang
- Nutrition Department, Clinical Center, NIH, Bethesda, MD, United States of America
| | - Claire M. Fraser
- Institute for Genome Sciences and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Lisa A. Farinelli
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Mehdi Farokhnia
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| | - Lorenzo Leggio
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, NIH, Baltimore, MD, United States of America
| |
Collapse
|
29
|
Lourenço KS, Suleiman AKA, Pijl A, Dimitrov MR, Cantarella H, Kuramae EE. Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments. MethodsX 2024; 12:102699. [PMID: 38660030 PMCID: PMC11041840 DOI: 10.1016/j.mex.2024.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).
Collapse
Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas 13020-902, SP, Brazil
| | - Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
- Soil Health group, Bioclear Earth B.V., Rozenburglaan 13, Groningen 9727 DL, The Netherlands
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
| | - Mauricio R. Dimitrov
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas 13020-902, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
30
|
Stefanello TB, Cardinal KM, Orso C, Franceschi CH, Silva JP, Mann MB, Frazzon J, Moraes PO, Ribeiro AML. The impact of different levels of functional oil supplementation in combination with salinomycin on growth performance and intestinal microbiota of broilers undergoing Eimeria challenge: An analysis of dynamics. Res Vet Sci 2024; 172:105249. [PMID: 38579633 DOI: 10.1016/j.rvsc.2024.105249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
The effect of salinomycin sodium alone and in combination with functional oils on performance and microbiota of broiler infected Eimeria were evaluated. 512 broilers were randomly assigned to 4 treatments (8 replicates, 16 birds/pen): a Control group (any additives); Ionophore group: salinomycin supplementation at 66 ppm (SS66); Ionophore +0.075% Functional oil (FO) group (SS66 + FO supplementation at 750 ppm); and Ionophore +0.10% FO group (SS66 + FO supplementation at 1000 ppm). At 14 days of age, birds were gavaged with 1 mL of a saline solution containing sporulated oocysts of E. tenella, E. acervulina and E. maxima. Performance indices were measured weekly. At 28 days, intestinal content was collected for microbiota analysis. Broilers of Control group presented the worst performance indices. Broilers of Ionophore + FO (0.075% and 0.10%) groups exhibited a higher BW at 28 days of age. The supplementation of Ionophore +0.075% FO resulted in a higher relative proportion of Firmicutes and a lower proportion of Actinobacteria in the ileum-jejunum. Lactobacillaceae was the dominant family in the jejunal, and ileal microbiotas of broilers fed diets supplemented with Ionophore, Ionophore +0.075% FO and Ionophore +0.10% FO. The supplementation of ionophore yielded higher numbers of Lactobacillaceae, Enterobactereaceae and Cloritridiaceae in the cecal. Ionophore associated with FO controlled the Lactobacillaceae, Enterobactereaceae and Cloritridiaceae families present in the cecum. Therefore, the combination of salinomycin with functional oil showed synergistic effect on performance and modulation of intestinal microbiota of broilers challenged with Eimeria.
Collapse
Affiliation(s)
- Thaís Bastos Stefanello
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Kátia Maria Cardinal
- Department of Animal Science, Instituto Federal Farroupilha, Alegrete, RS, Brazil
| | - Catiane Orso
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Jéssica Pereira Silva
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Micheli Bertoni Mann
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jeverzon Frazzon
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Priscila Oliveira Moraes
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | | |
Collapse
|
31
|
Yu Q, Liu Y, Liu S, Li S, Zhai Y, Zhang Q, Zheng L, Zheng H, Zhai Y, Wang X. Lactobacillus melliventris promotes hive productivity and immune functionality in Bombus terrestris performance in the greenhouse. INSECT SCIENCE 2024; 31:911-926. [PMID: 37830269 DOI: 10.1111/1744-7917.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
Bumblebees are important pollinators in agricultural ecosystems, but their abundance is declining globally. There is an urgent need to protect bumblebee health and their pollination services. Bumblebees possess specialized gut microbiota with potential to be used as probiotics to help defend at-risk bumblebee populations. However, evidence for probiotic benefits on bumblebees is lacking. Here, we evaluated how supplementation with Lactobacillus melliventris isolated from bumblebee gut affected the colony development of Bombus terrestris. This native strain colonized robustly and persisted long-term in bumblebees, leading to a significantly higher quality of offspring. Subsequently, the tyrosine pathway was upregulated in the brain and fat body, while the Wnt and mTOR pathways of the gut were downregulated. Notably, the field experiment in the greenhouse revealed the supplementation of L. melliventris led to a 2.5-fold increase in the bumblebee survival rate and a more than 10% increase in the number of flowers visited, indicating a better health condition and pollination ability in field conditions. Our study represents a first screening for the potential use of the native gut member, L. melliventris, as probiotic strains in hive supplement for bumblebee breeding, which may be a practical approach to improve immunity and hive health.
Collapse
Affiliation(s)
- Qianhui Yu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yan Liu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Shaogang Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yifan Zhai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qingchao Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiaofei Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| |
Collapse
|
32
|
Sarkar P, Chintaluri S, Sarkar S, Unnisa M, Jakkampudi A, Mulukutla AP, Kumari S, Reddy DN, Talukdar R. Evaluation of the Crosstalk Between the Host Mycobiome and Bacteriome in Patients with Chronic Pancreatitis. Indian J Microbiol 2024; 64:603-617. [PMID: 39011022 PMCID: PMC11246408 DOI: 10.1007/s12088-024-01207-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/14/2024] [Indexed: 07/17/2024] Open
Abstract
The human microbiome is a diverse consortium of microbial kingdoms that play pivotal roles in host health and diseases. We previously reported a dysbiotic bacteriome in chronic pancreatitis patients with diabetes (CPD) compared with patients with it's nondiabetic (CPND) phenotype. In this study, we extended our exploration to elucidate the intricate interactions between the mycobiome, bacteriome, and hosts' plasma metabolome with the disease phenotypes. A total of 25 participants (CPD, n = 7; CPND, n = 10; healthy control, n = 8) were recruited for the study. We observed elevated species richness in both the bacterial and fungal profiles within the CP diabetic cohort compared to the nondiabetic CP phenotype and healthy control cohorts. Notably, the CP group displayed heterogeneous fungal diversity, with only 40% of the CP nondiabetic patients and 20% of the CP diabetic patients exhibiting common core gut fungal profiles. Specific microbial taxa alterations were identified, including a reduction in Bifidobacterium adolescentis and an increase in the prevalence of Aspergillus penicilloides and Klebsiella sp. in the disease groups. In silico analysis revealed the enrichment of pathways related to lipopolysaccharide (LPS), apoptosis, and peptidase, as well as reduced counts of the genes responsible for carbohydrate metabolism in the CP groups. Additionally, distinct plasma metabolome signatures were observed, with CPD group exhibiting higher concentrations of sugars and glycerolipids, while the CPND cohort displayed elevated levels of amino acids in their blood. The fatty acid-binding protein (FABP) concentration was notably greater in the CPD group than in the HC group (4.220 vs. 1.10 ng/ml, p = 0.04). Furthermore, compared with healthy controls, disease groups exhibited fewer correlations between key fungal taxa (Aspergillus sp., Candida sp.) and bacterial taxa (Prevotella copri, Bifidobacteria sp., Rumminococcaceae). Our study unveils, for the first time, a dysbiotic mycobiome and emphasizes unique host bacterial-mycobial interactions in CP patient with diabetes, potentially influencing disease severity. These findings provide crucial insights for future mechanistic studies aiming to unravel the determinants of disease severity in this complex clinical context. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-024-01207-8.
Collapse
Affiliation(s)
- Priyanka Sarkar
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Sreelekha Chintaluri
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Subhaleena Sarkar
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Misbah Unnisa
- Department of Medical Gastroenterology, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Aparna Jakkampudi
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Ambika Prasanna Mulukutla
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Sneha Kumari
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - D. Nageshwar Reddy
- Department of Medical Gastroenterology, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| | - Rupjyoti Talukdar
- Gut Microbiome Research Group, Wellcome-DBT (Indian Alliance) Lab, Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
- Department of Medical Gastroenterology, Asian Institute of Gastroenterology (AIG Hospitals), Hyderabad, India
| |
Collapse
|
33
|
Iram A, Dong Y, Ignea C. Synthetic biology advances towards a bio-based society in the era of artificial intelligence. Curr Opin Biotechnol 2024; 87:103143. [PMID: 38781699 DOI: 10.1016/j.copbio.2024.103143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Synthetic biology is a rapidly emerging field with broad underlying applications in health, industry, agriculture, or environment, enabling sustainable solutions for unmet needs of modern society. With the very recent addition of artificial intelligence (AI) approaches, this field is now growing at a rate that can help reach the envisioned goals of bio-based society within the next few decades. Integrating AI with plant-based technologies, such as protein engineering, phytochemicals production, plant system engineering, or microbiome engineering, potentially disruptive applications have already been reported. These include enzymatic synthesis of new-to-nature molecules, bioelectricity generation, or biomass applications as construction material. Thus, in the not-so-distant future, synthetic biologists will help attain the overarching goal of a sustainable yet efficient production system for every aspect of society.
Collapse
Affiliation(s)
- Attia Iram
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
| | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.
| |
Collapse
|
34
|
Aya JV, Vega LC, Muñoz E, Muñoz M, López DF, Guzmán MP, Martínez DF, Cruz-Saavedra LB, Castillo AK, Quintero KJ, Gónzalez Soltero R, Cala MP, Ramírez JD. Divergent Gut Microbiota: Archaeal and Bacterial Signatures Unveil Unique Patterns in Colombian Cyclists Compared to Weightlifters and Non-Athletes. Adv Biol (Weinh) 2024; 8:e2400069. [PMID: 38548661 DOI: 10.1002/adbi.202400069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Indexed: 06/16/2024]
Abstract
Engagement in physical activity, across various sports, promotes a diverse microbiota in active individuals. This study examines the gut microbiota of Colombian athletes, specifically weightlifters (n = 16) and road cyclists (n = 13), compared to non-athletes (n = 15). Using Kruskal-Wallis tests, the physical activity level of a group of non-athletic individuals and the sports experience of a group of professional athletes is analyzed. The median age of participants is 24 years, comprising 25 men and 19 women. The microbiota is collected using fecal samples. Participants provided these samples during their pre-competitive stage, specifically during the concentration phase occurring two weeks prior to national competitions. This timing is chosen to capture the microbial composition during a period of heightened physical preparation. Questionnaire responses and microbial composition assessments identify disparities among groups. Microbial composition analysis explores core microbiome, abundance, and taxonomy using Pavian, MicrobiomeAnalyst 2.0, and GraPhlAn. ANCOM-BC2 reveals differentially abundant species. Road cyclists exhibit decreased Bacteria and increased Archaea abundance. Phylum-level variations included Planctomycetes, Acidobacteria, and Proteobacteria, while Bacteroidetes prevailed. Key families influencing gut microbiota are Bacteroidaceae, Muribaculaceae, and Selenomonadaceae. Weightlifters exhibit unique viral and archaeal community connections, while cyclists showed specialized microbial interplay influenced by endurance exercise. Correlation network analysis emphasizes distinctive microbial interactions within athlete groups, shedding light on the impact of physical activities on gut microbiota and athlete health.
Collapse
Affiliation(s)
- J V Aya
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - L C Vega
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - E Muñoz
- Universidad Santo Tomás, Bogotá, Colombia
| | - M Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Instituto de Biotecnología-UN (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
| | - D F López
- Centro Latinoamericano de Nutrición (CELAN), Bogotá, Colombia
| | - M P Guzmán
- Centro Latinoamericano de Nutrición (CELAN), Bogotá, Colombia
| | - D F Martínez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - L B Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - A K Castillo
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - K J Quintero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - R Gónzalez Soltero
- MAS Microbiota Group, Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Spain
| | - M P Cala
- MetCore - Metabolomics Core Facility, Vice-Presidency for Research, Universidad de los Andes, Bogotá, Colombia
| | - J D Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| |
Collapse
|
35
|
Horváthová T, Lafuente E, Bartels J, Wallisch J, Vorburger C. Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13252. [PMID: 38783543 PMCID: PMC11116767 DOI: 10.1111/1758-2229.13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.
Collapse
Affiliation(s)
- Terézia Horváthová
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Institute of Soil Biology and BiochemistryBiology Centre CASČeské BudějoviceCzechia
| | - Elvira Lafuente
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | | | | | - Christoph Vorburger
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- D‐USYS, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
| |
Collapse
|
36
|
Shibata H, Yamamoto K, Hirose T, Furune S, Kakushima N, Furukawa K, Nakamura M, Honda T, Fujishiro M, Kawashima H. Characteristics of microbiomes of the saliva, duodenal bulb, and descending portion of superficial nonampullary duodenal epithelial tumors. Dig Liver Dis 2024; 56:941-950. [PMID: 38413348 DOI: 10.1016/j.dld.2024.01.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
INTRODUCTION Nonampullary duodenal epithelial tumors are rare, but their prevalence is increasing. Various gastrointestinal cancers have been associated with microbiomes. We evaluated the characteristics of the salivary and duodenal microbiomes of patients with nonampullary duodenal epithelial tumors. METHODS Saliva and biopsy samples from the duodenal bulb and descending portion were obtained from 15 patients with nonampullary duodenal epithelial tumors and 10 controls. Next-generation sequencing was performed to identify bacteria for comparison. RESULTS Saliva samples had higher Amplicon Sequence Variants (ASVs) and more observed species than duodenal samples. Saliva samples from patients with nonampullary duodenal epithelial tumor were dominated by Bacteroidetes and Prevotella, whereas Proteobacteria and Neisseria were dominant in the control samples. The relative abundance of bacteria was higher in patients with nonampullary duodenal epithelial tumors. Most bacteria were classified as bacteria of oral origin. Oribacterium and Stomatobaculum were significantly higher in the saliva, duodenal bulb, and descending portion of patients with nonampullary duodenal epithelial tumors. CONCLUSION Patients with nonampullary duodenal epithelial tumors had different salivary and duodenal microbiomes than controls. Bacteria types differed between groups at each site, and most bacteria of oral origin were more abundant in patients with nonampullary duodenal epithelial tumors.
Collapse
Affiliation(s)
- Hiroyuki Shibata
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Kenta Yamamoto
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Takashi Hirose
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Satoshi Furune
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Naomi Kakushima
- Department of Gastroenterology, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kazuhiro Furukawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Masanao Nakamura
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan.
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Hiroki Kawashima
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 466-8550, Japan
| |
Collapse
|
37
|
Newman NK, Macovsky MS, Rodrigues RR, Bruce AM, Pederson JW, Padiadpu J, Shan J, Williams J, Patil SS, Dzutsev AK, Shulzhenko N, Trinchieri G, Brown K, Morgun A. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nat Protoc 2024; 19:1750-1778. [PMID: 38472495 DOI: 10.1038/s41596-024-00960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/29/2023] [Indexed: 03/14/2024]
Abstract
We present Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that offers a holistic view of biological systems by integrating data from multiple cohorts and diverse omics types. TkNA helps to decipher key players and mechanisms governing host-microbiota (or any multi-omic data) interactions in specific conditions or diseases. TkNA reconstructs a network that represents a statistical model capturing the complex relationships between different omics in the biological system. It identifies robust and reproducible patterns of fold change direction and correlation sign across several cohorts to select differential features and their per-group correlations. The framework then uses causality-sensitive metrics, statistical thresholds and topological criteria to determine the final edges forming the transkingdom network. With the subsequent network's topological features, TkNA identifies nodes controlling a given subnetwork or governing communication between kingdoms and/or subnetworks. The computational time for the millions of correlations necessary for network reconstruction in TkNA typically takes only a few minutes, varying with the study design. Unlike most other multi-omics approaches that find only associations, TkNA focuses on establishing causality while accounting for the complex structure of multi-omic data. It achieves this without requiring huge sample sizes. Moreover, the TkNA protocol is user friendly, requiring minimal installation and basic familiarity with Unix. Researchers can access the TkNA software at https://github.com/CAnBioNet/TkNA/ .
Collapse
Affiliation(s)
- Nolan K Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | | | - Richard R Rodrigues
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Amanda M Bruce
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jacob W Pederson
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Jyothi Padiadpu
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jigui Shan
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua Williams
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sankalp S Patil
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Amiran K Dzutsev
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Natalia Shulzhenko
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Kevin Brown
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
| |
Collapse
|
38
|
Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024; 15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.
Collapse
Affiliation(s)
- Carlos Willian Dias Dantas
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - David Tavares Martins
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Oscar Victor Cardenas Alegria
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| |
Collapse
|
39
|
Repkin EA, Gafarova ER, Varfolomeeva MA, Kurjachii DS, Polev DE, Shavarda AL, Maslakov GP, Mullakhmetov RI, Zubova EV, Bariev TB, Granovitch AI, Maltseva AL. Littorina snails and Microphallus trematodes: Diverse consequences of the trematode-induced metabolic shifts. Parasitol Res 2024; 123:229. [PMID: 38819740 DOI: 10.1007/s00436-024-08244-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 05/18/2024] [Indexed: 06/01/2024]
Abstract
The intricate relationships between parasites and hosts encompass a wide range of levels, from molecular interactions to population dynamics. Parasites influence not only the physiological processes in the host organism, but also the entire ecosystem, affecting mortality of individuals, the number of offspring through parasitic castration, and matter and energy cycles. Understanding the molecular mechanisms that govern host-parasite relationships and their impact on host physiology and environment remains challenging. In this study, we analyzed how infection with Microphallus trematodes affects the metabolome of two Littorina snail species inhabiting different intertidal zone shore levels. We applied non-targeted GC-MS-based metabolomics to analyze biochemical shifts induced by trematode infection in a host organism. We have identified changes in energy, amino acid, sugar, and lipid metabolism. In particular, we observed intensified amino acid catabolism and nitrogenous catabolites (glutamine, urea) production. These changes primarily correlated with infection and interspecies differences of the hosts rather than shore level. The changes detected in the host metabolism indicate that other aspects of life may have been affected, both within the host organism and at a supra-organismal level. Therefore, we explored changes in microbiota composition, deviations in the host molluscs behavior, and acetylcholinesterase activity (ACE, an enzyme involved in neuromuscular transmission) in relation to infection. Infected snails displayed changes in their microbiome composition. Decreased ACE activity in snails was associated with reduced mobility, but whether it is associated with trematode infection remains unclear. The authors suggest a connection between the identified biochemical changes and the deformation of the shell of molluscs, changes in their behavior, and the associated microbiome. The role of parasitic systems formed by microphallid trematodes and Littorina snails in the nitrogen cycle at the ecosystem level is also assumed.
Collapse
Affiliation(s)
- Egor A Repkin
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia.
- Research Park Centre for Molecular and Cell Technologies, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia.
| | - Elizaveta R Gafarova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Dmitrii S Kurjachii
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Dmitrii E Polev
- Department of Epidemiology, St. Petersburg Pasteur Institute, 197101 Mira Street 14, St. Petersburg, Russia
| | - Alexei L Shavarda
- Research Park Centre for Molecular and Cell Technologies, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
- Department of Analytical Phytochemistry, Komarov Botanical Institute, 197376 Professora Popova Street 2, St. Petersburg, Russia
| | - Georgiy P Maslakov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Roman I Mullakhmetov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Ekaterina V Zubova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Timur B Bariev
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 Universitetskaya Emb. 7/9, St. Petersburg, Russia
| |
Collapse
|
40
|
Minaya DM, Kim JS, Kirkland R, Allen J, Cullinan S, Maclang N, de Lartigue G, de La Serre CB. Transfer with microbiota from lean donors prevents excessive weight gain and restores gut-brain vagal signaling in obese rats maintained on a high fat diet. RESEARCH SQUARE 2024:rs.3.rs-4438240. [PMID: 38853960 PMCID: PMC11160927 DOI: 10.21203/rs.3.rs-4438240/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background The collection of microorganisms, mainly bacteria, which live in the gastrointestinal (GI) tract are collectible known as the gut microbiota. GI bacteria play an active role in regulation of the host's immune system and metabolism, as well as certain pathophysiological processes. Diet is the main factor modulating GI microbiota composition and recent studies have shown that high fat (HF) diets induce detrimental changes, known as dysbiosis, in the GI bacterial makeup. HF diet induced microbiota dysbiosis has been associated with structural and functional changes in gut-brain vagally mediated signaling system, associated with overeating and obesity. Although HF-driven changes in microbiota composition are sufficient to alter vagal signaling, it is unknown if restoring normal microbiota in obesity can improve gut-brain signaling and metabolic outcomes. In this study, we evaluated the effect of lean gut microbiota transfer in obese, vagally compromised, rats on gut-brain communication, food intake, and body weight. Male Sprague-Dawley rats were maintained on regular chow, or 45% HF diet for nine weeks followed by three weeks of microbiota depletion using an antibiotic cocktail. The animals were then divided into four groups (n=10 each): LF - control group on regular chow, LF-LF - chow fed animals that received antibiotics and microbiota from chow fed animals, HF-LF - HF fed animals that received microbiota from chow fed animals, and HF-HF - HF fed animals that received microbiota from HF fed animals. Animals were gavaged with donor microbiota for three consecutive days on week one and once a week thereafter for three more weeks. HF-LF animals received inulin as a prebiotic to aid the establishment of the lean microbiome. Results We found that transferring a LF microbiota to HF fed animals (HF-LF) reduced caloric intake during the light phase when compared with HF-HF rats and prevented additional excessive weight gain. We did not observe significant changes in the density of vagal afferents terminating in the brainstem among the groups, however, HF-LF animals displayed an increase in postprandial activation of both primary sensory neurons innervating the GI tract and brainstem secondary neurons. Conclusions We concluded from these data that normalizing microbiota composition in obese rats improves gut-brain communication and restores normal feeding patterns which was associated with a reduction in weight gain.
Collapse
Affiliation(s)
- Dulce M. Minaya
- Department of Nutritional Science, University of Georgia, Athens, GA
| | | | - Rebecca Kirkland
- Department of Nutritional Science, University of Georgia, Athens, GA
| | - Jillian Allen
- Department of Nutritional Science, University of Georgia, Athens, GA
| | - Sitara Cullinan
- Department of Nutritional Science, University of Georgia, Athens, GA
| | - Neil Maclang
- Department of Nutritional Science, University of Georgia, Athens, GA
| | | | | |
Collapse
|
41
|
Liu Y, Wang X, Zeng D, Wang H, Ma Y, Zhao X, Guan Z, Ning Z, Qu L. Temporal variation in production performance, biochemical and oxidative stress markers, and gut microbiota in Pekin ducks during the late growth stage. Poult Sci 2024; 103:103894. [PMID: 39013293 DOI: 10.1016/j.psj.2024.103894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 07/18/2024] Open
Abstract
In the late growth stage of commercial Pekin ducks, a significant increase in feed intake and a decline in body weight gain have been observed, leading to impaired feed conversion efficiency. To address this issue, we investigated alterations in production performance, blood biochemical indices, ileum tissue architecture, and microbial community structure in Pekin ducks. The primary objective was to provide robust data supporting the improvement of meat duck production efficiency during the late growth stage (28-42-days-old). Forty 28-day-old Pekin ducks were randomly assigned to 8 replicates, with five ducks per replicate. The rearing period lasted 14 days, with feed and water provided ad libitum. Our findings indicated a significant increase in Pekin duck body and heart weights with advancing age (P < 0.05). Moreover, serum antioxidant enzyme and high-density lipoprotein concentrations significantly increased, whereas triglyceride levels decreased (P < 0.05). Notably, the height of the ileal villi was significantly reduced (P < 0.05). The microbial community structure of the ileum exhibited significant changes as ducks aged, accompanied by a substantial increase in microbial flora diversity, particularly with the formation of more tightly connected microbial network modules. Time-dependent enrichment was observed in microbial gene functions related to energy metabolism pathways. At the genus level, Sphingomonas and Subdoligranulum have emerged as crucial players in microbial differential functional pathways and network formation. These bacteria likely serve as the key driving factors in the dynamic microbial changes that occur in Pekin ducks over time. Overall, our findings suggest a potential decline in the absorption function of the small intestine and fat deposition performance of Pekin ducks during later growth stages, which may be attributed to the maturation and proliferation of the gut microbial community.
Collapse
Affiliation(s)
- Yuchen Liu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xintong Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Dan Zeng
- Huayu Agricultural Science and Technology Co., Ltd., Handan, China
| | - Haiyan Wang
- Technical Center of Hohhot Customs, Huhhot, Inner Mongolia, China
| | - Ying Ma
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zi Guan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
42
|
Tsholo K, Molale-Tom LG, Horn S, Bezuidenhout CC. Distribution of antibiotic resistance genes and antibiotic residues in drinking water production facilities: Links to bacterial community. PLoS One 2024; 19:e0299247. [PMID: 38781192 PMCID: PMC11115235 DOI: 10.1371/journal.pone.0299247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/06/2024] [Indexed: 05/25/2024] Open
Abstract
There is a rapid spread of antibiotic resistance in the environment. However, the impact of antibiotic resistance in drinking water is relatively underexplored. Thus, this study aimed to quantify antibiotic resistance genes (ARGs) and antibiotic residues in two drinking water production facilities (NW-E and NW-C) in North West Province, South Africa and link these parameters to bacterial communities. Physicochemical and ARG levels were determined using standard procedures. Residues (antibiotics and fluconazole) and ARGs were quantified using ultra-high performance liquid chromatography (UHPLC) chemical analysis and real-time PCR, respectively. Bacterial community compositions were determined by high-throughput 16S rRNA sequencing. Data were analysed using redundancy analysis and pairwise correlation. Although some physicochemical levels were higher in treated than in raw water, drinking water in NW-E and NW-C was safe for human consumption using the South African Water Quality Guideline (SAWQG). ARGs were detected in raw and treated water. In NW-E, the concentrations of ARGs (sul1, intl1, EBC, FOX, ACC and DHA) were higher in treated water than in raw water. Regarding antimicrobial agents, antibiotic and fluconazole concentrations were higher in raw than in treated water. However, in NW-C, trimethoprim concentrations were higher in raw than in treated water. Redundancy analysis showed that bacterial communities were not significantly correlated (Monte Carlo simulations, p-value >0.05) with environmental factors. However, pairwise correlation showed significant differences (p-value <0.05) for Armatimonas, CL500-29 marine group, Clade III, Dickeya and Zymomonas genera with environmental factors. The presence of ARGs and antibiotic residues in the current study indicated that antibiotic resistance is not only a clinical phenomenon but also in environmental settings, particularly in drinking water niches. Consumption of NW-E and NW-C treated water may facilitate the spread of antibiotic resistance among consumers. Thus, regulating and monitoring ARGs and antibiotic residues in drinking water production facilities should be regarded as paramount.
Collapse
Affiliation(s)
- Karabo Tsholo
- Unit for Environmental Sciences and Management – Microbiology, North-West University, Potchefstroom, South Africa
| | - Lesego Gertrude Molale-Tom
- Unit for Environmental Sciences and Management – Microbiology, North-West University, Potchefstroom, South Africa
| | - Suranie Horn
- Unit for Environmental Sciences and Management – Microbiology, North-West University, Potchefstroom, South Africa
- Occupational Hygiene and Health Research Initiative (OHHRI), Faculty of Health Science, North-West University, Private Bag X6001, Potchefstroom, South Africa
| | | |
Collapse
|
43
|
Nath AR, Natarajan J. Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers. Genomics Inform 2024; 22:1. [PMID: 38907281 PMCID: PMC11184957 DOI: 10.1186/s44342-024-00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/07/2024] [Indexed: 06/23/2024] Open
Abstract
The goal of the study was to investigate the changes in the gut microbiota during the advancement of gastric cancer (GC) and identify pertinent taxa associated with the disease. We used a public fecal amplicon gastric cancer dataset from the Sequence Retrieval Archive (SRA), of patients with GC, gastritis, and healthy individuals. We did sequence pre-processing, including quality filtering of the sequences. Then, we performed a diversity analysis, evaluating α- and β-diversity. Next, taxonomic composition analysis was performed and the relative abundances of different taxa at the phylum and genus levels were compared between GC, gastritis, and healthy controls. The obtained results were subsequently subjected to statistical validation. To conclude, metagenomic function prediction was carried out, followed by correlation analysis between the microbiota and KEGG pathways. α analysis revealed a significant difference between male and female categories, while β analysis demonstrated significant distinctions between GC, gastritis, and healthy controls, as well as between sexes within the GC and gastritis groups. The statistically confirmed taxonomic composition analysis highlighted the presence of the microbes Bacteroides and Veillonella. Furthermore, through metagenomic prediction analysis and correlation analysis with pathways, three taxa, namely Akkermansia, Gammaproteobacteria, and Veillonella, were identified as potential biomarkers for GC. Additionally, this study reports, for the first time, the presence of two bacteria, Desulfobacteriota and Synergistota, in GC, necessitating further investigation. Overall, this research sheds light on the potential involvement of gut microbiota in GC pathophysiology; however, additional studies are warranted to explore its functional significance.
Collapse
Affiliation(s)
- Anju R Nath
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046, India.
| |
Collapse
|
44
|
Kumar A, Sharma S, Dindhoria K, Thakur A, Kumar R. Insight into physico-chemical properties and microbial community structure of biogas slurry from household biogas plants of sub-Himalaya for its implications in improved biogas production. Int Microbiol 2024:10.1007/s10123-024-00530-w. [PMID: 38760649 DOI: 10.1007/s10123-024-00530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Numerous metagenomics studies, conducted in both full-scale anaerobic digesters and household biogas plants, have shed light on the composition and activity of microbial flora essential for optimizing the performance of biogas reactors, underscoring the significance of microbial community composition in biogas plant efficiency. Although the efficiency of household biogas plants in the sub-Himalayan region has been reported, there is no literature evidence on the microbial community structure of such household biogas plants in the sub-Himalayan region. The current study evaluated the physico-chemical properties and bacterial community structure from the slurry samples of household biogas plants prevalent in the sub-Himalayan region. The slurry samples were observed to be rich in nutrients; however, their carbon and nitrogen contents were higher than the recommended standard values of liquid-fermented organic manure. The species richness and diversity indices (Chao1, Shannon, and Simpson) of household biogas plants were quite similar to the advanced biogas reactors operating at mesophilic conditions. 16S rRNA gene amplicon sequencing reveals microbial diversity, showing a higher abundance of Firmicutes (70.9%) and Euryarchaeota (9.52%) in advanced biogas reactors compared to household biogas plants. Microbial analysis shows a lack of beneficial microbes for anaerobic digestion, which might be the reason for inefficient biogas production in household biogas plants of the sub-Himalayan region. The lack of efficient bacterial biomass may also be attributed to the digester design, feedstock, and ambient temperatures. This study emphasized the establishment of efficient microbial consortia for enhanced degradation rates that may increase the methane yield in biogas plants.
Collapse
Affiliation(s)
- Aman Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sonia Sharma
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Kiran Dindhoria
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aman Thakur
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakshak Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
| |
Collapse
|
45
|
de Sousa LP, Mondego JMC. Leaf surface microbiota transplantation confers resistance to coffee leaf rust in susceptible Coffea arabica. FEMS Microbiol Ecol 2024; 100:fiae049. [PMID: 38599638 PMCID: PMC11141781 DOI: 10.1093/femsec/fiae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/10/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024] Open
Abstract
Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.
Collapse
Affiliation(s)
- Leandro Pio de Sousa
- Instituto Agronômico, Centro de Pesquisa e Desenvolvimento de Recursos Genéticos Vegetais, Campinas, 13020-902 São Paulo, Brazil
| | - Jorge Maurício Costa Mondego
- Instituto Agronômico, Centro de Pesquisa e Desenvolvimento de Recursos Genéticos Vegetais, Campinas, 13020-902 São Paulo, Brazil
| |
Collapse
|
46
|
Jiménez-Ríos L, Torrado A, González-Pimentel JL, Iniesta-Pallarés M, Molina-Heredia FP, Mariscal V, Álvarez C. Emerging nitrogen-fixing cyanobacteria for sustainable cotton cultivation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171533. [PMID: 38458446 DOI: 10.1016/j.scitotenv.2024.171533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Amid growing environmental concerns and the imperative for sustainable agricultural practices, this study examines the potential of nitrogen-fixing cyanobacteria as biofertilizers, particularly in cotton cultivation. The reliance on synthetic nitrogen fertilizers (SNFs), prevalent in modern agriculture, poses significant environmental challenges, including greenhouse gas emissions and water system contamination. This research aims to shift this paradigm by exploring the capacity of cyanobacteria as a natural and sustainable alternative. Utilizing advanced metabarcoding methods to analyze the 16S rRNA gene, we conducted a comprehensive assessment of soil bacterial communities within cotton fields. This study focused on evaluating the diversity, structure, taxonomic composition, and potential functional characteristics of these communities. Emphasis was placed on the isolation of native N2-fixing cyanobacteria strains rom cotton soils, and their subsequent effects on cotton growth. Results from our study demonstrate significant plant growth-promoting (PGP) activities, measured as N2 fixation, production of Phytohormones, Fe solubilization and biofertilization potential of five isolated cyanobacterial strains, underscoring their efficacy in cotton. These findings suggest a viable pathway for replacing chemical-synthetic nitrogen fertilizers with natural, organic alternatives. The reintegration of these beneficial species into agricultural ecosystems can enhance crop growth while fostering a balanced microbial environment, thus contributing to the broader goals of global sustainable agriculture.
Collapse
Affiliation(s)
- Lucía Jiménez-Ríos
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Alejandro Torrado
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - José Luis González-Pimentel
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Macarena Iniesta-Pallarés
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
| |
Collapse
|
47
|
Schluter J, Hussey G, Valeriano J, Zhang C, Sullivan A, Fenyö D. The MTIST platform: a microbiome time series inference standardized test. RESEARCH SQUARE 2024:rs.3.rs-4343683. [PMID: 38766187 PMCID: PMC11100882 DOI: 10.21203/rs.3.rs-4343683/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The human gut microbiome is a promising therapeutic target, but interventions are hampered by our limited understanding of microbial ecosystems. Here, we present a platform to develop, evaluate, and score approaches to learn ecological interactions from microbiome time series data. The microbiome time series inference standardized test (MTIST) comprises: a simulation framework for the in silico generation of microbiome study data akin to what is obtained with quantitative next-generation sequencing approaches, a compilation of a large curated data set generated by the simulation framework representing 648 simulated microbiome studies containing 18,360 time series, with a total of 2,182,800 species abundance measurements, and a scoring method to rank ecological inference algorithms. We use the MTIST platform to rank five implementations of microbiome inference approaches, revealing that while all algorithms performed well on ecosystems with few species (3 and 10), all algorithms failed to infer most interaction in a large ecosystem with 100 member species. However, we do find that the strongest interactions within a large ecosystem are inferred with higher success by all algorithms. Finally, we use the MTIST platform to compare different microbiome study designs, characterizing tradeoffs between samples per subject and number of subjects. Interestingly, we find that when only few samples can be collected per subject, ecological inference is most successful when these samples are collected with highest feasible temporal frequency. Taken together, we provide a computational tool to aid the development of better microbiome ecosystem inference approaches, which will be crucial towards the development of reliable and predictable therapeutic approaches that target the microbiome ecosystem.
Collapse
Affiliation(s)
| | | | - João Valeriano
- Centre Interdisciplinaire de Nanoscience de Marseille, Aix-Marseille Université
| | | | | | | |
Collapse
|
48
|
Sidiropoulos T, Dovrolis N, Katifelis H, Michalopoulos NV, Kokoropoulos P, Arkadopoulos N, Gazouli M. Dysbiosis Signature of Fecal Microbiota in Patients with Pancreatic Adenocarcinoma and Pancreatic Intraductal Papillary Mucinous Neoplasms. Biomedicines 2024; 12:1040. [PMID: 38791002 PMCID: PMC11117863 DOI: 10.3390/biomedicines12051040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Pancreatic cancer (PC) ranks as the seventh leading cause of cancer-related deaths, with approximately 500,000 new cases reported in 2020. Existing strategies for early PC detection primarily target individuals at high risk of developing the disease. Nevertheless, there is a pressing need to identify innovative clinical approaches and personalized treatments for effective PC management. This study aimed to explore the dysbiosis signature of the fecal microbiota in PC and potential distinctions between its Intraductal papillary mucinous neoplasm (IPMN) and pancreatic ductal adenocarcinoma (PDAC) phenotypes, which could carry diagnostic significance. The study enrolled 33 participants, including 22 diagnosed with PDAC, 11 with IPMN, and 24 healthy controls. Fecal samples were collected and subjected to microbial diversity analysis across various taxonomic levels. The findings revealed elevated abundances of Firmicutes and Proteobacteria in PC patients, whereas healthy controls exhibited higher proportions of Bacteroidota. Both LEfSe and Random Forest analyses indicated the microbiome's potential to effectively distinguish between PC and healthy control samples but fell short of differentiating between IPMN and PDAC samples. These results contribute to the current understanding of this challenging cancer type and highlight the applications of microbiome research. In essence, the study provides clear evidence of the gut microbiome's capability to serve as a biomarker for PC detection, emphasizing the steps required for further differentiation among its diverse phenotypes.
Collapse
Affiliation(s)
- Theodoros Sidiropoulos
- 4th Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece; (T.S.); (N.V.M.); (P.K.); (N.A.)
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.D.); (H.K.)
| | - Hector Katifelis
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.D.); (H.K.)
| | - Nikolaos V. Michalopoulos
- 4th Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece; (T.S.); (N.V.M.); (P.K.); (N.A.)
| | - Panagiotis Kokoropoulos
- 4th Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece; (T.S.); (N.V.M.); (P.K.); (N.A.)
| | - Nikolaos Arkadopoulos
- 4th Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece; (T.S.); (N.V.M.); (P.K.); (N.A.)
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.D.); (H.K.)
| |
Collapse
|
49
|
Tang XF, Sun YF, Liang YS, Yang KY, Chen PT, Li HS, Huang YH, Pang H. Metabolism, digestion, and horizontal transfer: potential roles and interaction of symbiotic bacteria in the ladybird beetle Novius pumilus and their prey Icerya aegyptiaca. Microbiol Spectr 2024; 12:e0295523. [PMID: 38497713 PMCID: PMC11064573 DOI: 10.1128/spectrum.02955-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
In this study, we first time sequenced and analyzed the 16S rRNA gene data of predator ladybird beetles Novius pumilus and globally distributed invasive pest Icerya aegyptiaca at different stages, and combined data with bacterial genome sequences in N. pumilus to explored the taxonomic distribution, alpha and beta diversity, differentially abundant bacteria, co-occurrence network, and putative functions of their microbial community. Our finding revealed that Candidatus Walczuchella, which exhibited a higher abundance in I. aegyptiaca, possessed several genes in essential amino acid biosynthesis and seemed to perform roles in providing nutrients to the host, similar to other obligate symbionts in scale insects. Lactococcus, Serratia, and Pseudomonas, more abundant in N. pumilus, were predicted to have genes related to hydrocarbon, fatty acids, and chitin degradation, which may assist their hosts in digesting the wax shell covering the scale insects. Notably, our result showed that Lactococcus had relatively higher abundances in adults and eggs compared to other stages in N. pumilus, indicating potential vertical transmission. Additionally, we found that Arsenophonus, known to influence sex ratios in whitefly and wasp, may also function in I. aegyptiaca, probably by influencing nutrient metabolism as it similarly had many genes corresponding to vitamin B and essential amino acid biosynthesis. Also, we observed a potential horizontal transfer of Arsenophonus between the scale insect and its predator, with a relatively high abundance in the ladybirds compared to other bacteria from the scale insects.IMPORTANCEThe composition and dynamic changes of microbiome in different developmental stages of ladybird beetles Novius pumilus with its prey Icerya aegyptiaca were detected. We found that Candidatus Walczuchella, abundant in I. aegyptiaca, probably provide nutrients to their host based on their amino acid biosynthesis-related genes. Abundant symbionts in N. pumilus, including Lactococcus, Serratia, and Pseudophonus, may help the host digest the scale insects with their hydrocarbon, fatty acid, and chitin degrading-related genes. A key endosymbiont Arsenophonus may play potential roles in the nutrient metabolisms and sex determination in I. aegyptiaca, and is possibly transferred from the scale insect to the predator.
Collapse
Affiliation(s)
- Xue-Fei Tang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yi-Fei Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuan-Sen Liang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Kun-Yu Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Pei-Tao Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
50
|
Aljabr W, Dandachi I, Abbas B, Karkashan A, Al-Amari A, AlShahrani D. Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities. Microbiol Spectr 2024; 12:e0416623. [PMID: 38557102 PMCID: PMC11237758 DOI: 10.1128/spectrum.04166-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/24/2024] [Indexed: 04/04/2024] Open
Abstract
Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.
Collapse
Affiliation(s)
- Waleed Aljabr
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iman Dandachi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Basma Abbas
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Alaa Karkashan
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ahod Al-Amari
- Department of Basic Medical Sciences, College of Medicine, Dar Al-Uloom University, Riyadh, Saudi Arabia
| | - Dayel AlShahrani
- Pediatric infectious diseases, King Fahad Medical City, Riyadh, Saudi Arabia
| |
Collapse
|