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Alencar RM, Martínez JG, Machado VN, Alzate JF, Ortiz-Ojeda CP, Matias RR, Benzaquem DC, Santos MCF, Assunção EN, Lira EC, Astolfi-Filho S, Hrbek T, Farias IP, Fantin C. Preliminary profile of the gut microbiota from amerindians in the Brazilian amazon experiencing a process of transition to urbanization. Braz J Microbiol 2024:10.1007/s42770-024-01413-y. [PMID: 38913252 DOI: 10.1007/s42770-024-01413-y] [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: 03/13/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024] Open
Abstract
The Yanomami are one of the oldest indigenous tribes in the Amazon and are direct descendants of the first people to colonize South America 12,000 years ago. They are located on the border between Venezuela and Brazil, with the Venezuelan side remaining uncontacted. While they maintain a hunter-gatherer society, they are currently experiencing contact with urbanized populations in Brazil. The human gut microbiota of traditional communities has become the subject of recent studies due to the Westernization of their diet and the introduction of antibiotics and other chemicals, which have affected microbial diversity in indigenous populations, thereby threatening their existence. In this study, we preliminarily characterized the diversity of the gut microbiota of the Yanomami, a hunter-gatherer society from the Amazon, experiencing contact with urbanized populations. Similarly, we compared their diversity with the population in Manaus, Amazonas. A metabarcoding approach of the 16 S rRNA gene was carried out on fecal samples. Differences were found between the two populations, particularly regarding the abundance of genera (e.g., Prevotella and Bacteroides) and the higher values of the phyla Bacteroidetes over Firmicutes, which were significant only in the Yanomami. Some bacteria were found exclusively in the Yanomami (Treponema and Succinivibrio). However, diversity was statistically equal between them. In conclusion, the composition of the Yanomami gut microbiota still maintains the profile characteristic of a community with a traditional lifestyle. However, our results suggest an underlying Westernization process of the Yanomami microbiota when compared with that of Manaus, which must be carefully monitored by authorities, as the loss of diversity can be a sign of growing danger to the health of the Yanomami.
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Affiliation(s)
- Rodrigo M Alencar
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - José G Martínez
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil.
- Grupo de investigación Biociencias, Facultad de Ciencias de la Salud, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia.
| | - Valéria N Machado
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
| | - Juan F Alzate
- National Center for Genomic Sequencing, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Cinthya P Ortiz-Ojeda
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
- Universidad Tecnológica del Perú, Lima, Peru
| | - Rosiane R Matias
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Denise C Benzaquem
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Maria C F Santos
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Enedina N Assunção
- Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Manaus, Brazil
| | - Evelyn C Lira
- Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Manaus, Brazil
| | | | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, USA
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
| | - Cleiton Fantin
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, Brazil
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Chen YY, Tan L, Su XL, Chen NX, Liu Q, Feng YZ, Guo Y. NOD2 contributes to Parvimonas micra-induced bone resorption in diabetic rats with experimental periodontitis. Mol Oral Microbiol 2024. [PMID: 38757737 DOI: 10.1111/omi.12467] [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: 02/15/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) may affect the oral microbial community, exacerbating periodontal inflammation; however, its pathogenic mechanisms remain unclear. As nucleotide-binding oligomerization domain 2 (NOD2) plays a crucial role in the activation during periodontitis (PD), it is hypothesized that changes in the oral microbial community due to diabetes enhance periodontal inflammation through the activation of NOD2. METHODS We collected subgingival plaque from 180 subjects who were categorized into two groups based on the presence or absence of T2DM. The composition of oral microbiota was detected by 16S rRNA high-throughput sequencing. In animal models of PD with or without T2DM, we assessed alveolar bone resorption by micro-computerized tomography and used immunohistochemistry to detect NOD2 expression in alveolar bone. Primary osteoblasts were cultured in osteogenic induction medium with high or normal glucose and treated with inactivated bacteria. After 24 h of inactivated bacteria intervention, the osteogenic differentiation ability was detected by alkaline phosphatase (ALP) staining, and the expressions of NOD2 and interleukin-12 (IL-6) were detected by western blot. RESULTS The relative abundance of Parvimonas and Filifactor in the T2DM group was increased compared to the group without T2DM. In animal models, alveolar bone mass was decreased in PD, particularly in T2DM with PD (DMPD) group, compared to controls. Immunohistochemistry revealed NOD2 in osteoblasts from the alveolar bone in both the PD group and DMPD group, especially in the DMPD group. In vitro, intervention with inactivated Parvimonas significantly reduced ALP secretion of primary osteoblasts in high glucose medium, accompanied by increased expression of NOD2 and IL-6. CONCLUSIONS The results suggest that T2DM leading to PD may be associated with the activation of NOD2 by Parvimonas.
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Affiliation(s)
- Ying-Yi Chen
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- Department of Stomatology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences(Qingdao Central Hospital), Qingdao, China
| | - Li Tan
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Lin Su
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ning-Xin Chen
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiong Liu
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yun-Zhi Feng
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yue Guo
- Hunan Provincial Clinical Research Center for Oral Diseases, Hunan Provincial Engineering Research Center of Digital Oral and Maxillofacial Defect Repair, Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
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Favale N, Farina R, Carrieri A, Simonelli A, Severi M, Sabbioni S, Trombelli L, Scapoli C. Functional profile of oral plaque microbiome: Further insight into the bidirectional relationship between type 2 diabetes and periodontitis. Mol Oral Microbiol 2024; 39:62-79. [PMID: 37257865 DOI: 10.1111/omi.12418] [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: 11/23/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Increasing evidence support the association between the oral microbiome and human systemic diseases. This association may be attributed to the ability of many oral microbes to influence the inflammatory microenvironment. Herein, we focused our attention on the bidirectional relationship between periodontitis and type 2 diabetes using high-resolution whole metagenomic shotgun analysis to explore the composition and functional profile of the subgingival microbiome in diabetics and non-diabetics subjects with different periodontal conditions. In the present study, the abundance of metabolic pathways encoded by oral microbes was reconstructed from the metagenome, and we identified a set of dysregulated metabolic pathways significantly enriched in the periodontitis and/or diabetic patients. These pathways were mainly involved in branched and aromatic amino acids metabolism, fatty acid biosynthesis and adipocytokine signaling pathways, ferroptosis and iron homeostasis, nucleotide metabolism, and finally in the peptidoglycan and lipopolysaccharides synthesis. Overall, the results of the present study provide evidence in favor of the hypothesis that during the primary inflammatory challenge, regardless of whether it is induced by periodontitis or diabetes, endotoxemia and/or the release of inflammatory cytokines cause a change in precursor and/or in circulating innate immune cells. Dysbiosis and inflammation, also via oral-gut microbiome axis or adipose tissue, reduce the efficacy of the host immune response, while fueling inflammation and can induce that metabolic/epigenetic reprogramming of chromatin accessibility of genes related to the immune response. Moreover, the presence of an enhanced ferroptosis and an imbalance in purine/pyrimidine metabolism provides new insights into the role of ferroptotic death in this comorbidity.
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Affiliation(s)
- Nicoletta Favale
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Roberto Farina
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Alberto Carrieri
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Anna Simonelli
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Mattia Severi
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Silvia Sabbioni
- Department of Life Sciences and Biotechnology - Section of Pathology and Applied Microbiology, University of Ferrara, Ferrara, Italy
| | - Leonardo Trombelli
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Ferrara, Italy
- Operative Unit of Dentistry, Azienda Unità Sanitaria Locale (A.U.S.L.), Ferrara, Italy
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Ferrara, Italy
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Virendra A, Gulavane SU, Ahmed ZA, Reddy R, Chaudhari RJ, Gaikwad SM, Shelar RR, Ingole SD, Thorat VD, Khanam A, Khan FA. Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis. Vet Med Sci 2024; 10:e1369. [PMID: 38357732 PMCID: PMC10867593 DOI: 10.1002/vms3.1369] [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: 05/26/2023] [Revised: 12/10/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND The application of high throughput technologies has enabled unravelling of unique differences between healthy mares and mares with endometritis at transcriptomic and proteomic levels. However, differences in the uterine microbiome are yet to be investigated. OBJECTIVES The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis. METHODS Low-volume lavage (LVL) samples were collected from the uterus of 30 mares classified into healthy (n = 15) and endometritis (n = 15) based on their reproductive history, intrauterine fluid accumulation, gross appearance of LVL samples, endometrial cytology and bacterial culture. The samples were subjected to 16S rRNA sequencing. RESULTS Notable differences in the uterine microbiome were observed between healthy mares and mares with endometritis at various taxonomic levels. In healthy mares, the most abundant phylum, class, order and family were Firmicutes, Bacilli, Bacillales and Paenibacillaceae, respectively. In contrast, the most abundant corresponding taxonomic levels in mares with endometritis were Proteobacteria, Gammaproteobacteria, Enterobacterales and Enterobacteriaceae, respectively. At the genus level, Brevibacillus and Paenibacillus were more abundant in healthy mares, whereas Escherichia, Salmonella and Klebsiella were more abundant in mares with endometritis. In healthy mares, Brevibacillus brevis was the most abundant species, followed by Brevibacillus choshinensis and Paenibacillus sp JDR-2. However, in mares with endometritis, Escherichia coli was the most abundant species, followed by Salmonella enterica and Klebsiella pneumoniae. CONCLUSIONS These results confirmed the previously reported presence of a uterine microbiome in healthy mares and helped unravel some alterations that occur in mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.
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Affiliation(s)
- Aeknath Virendra
- Department of Animal ReproductionGynecology and ObstetricsMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | - Sarita U. Gulavane
- Department of Animal ReproductionGynecology and ObstetricsMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | | | - Ravi Reddy
- Nanoli Stud and Agricultural FarmPuneMaharashtraIndia
| | - Ravindra J. Chaudhari
- Department of Animal ReproductionGynecology and ObstetricsMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | - Sandeep M. Gaikwad
- Department of Animal ReproductionGynecology and ObstetricsMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | - Raju R. Shelar
- Department of Animal ReproductionGynecology and ObstetricsMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | - Shailesh D. Ingole
- Department of Veterinary PhysiologyMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | - Varsha D. Thorat
- Department of Veterinary MicrobiologyMumbai Veterinary CollegeMumbaiMaharashtraIndia
| | - Afroza Khanam
- Department of Large Animal Medicine and SurgerySchool of Veterinary MedicineSt. George's UniversityGrenadaWest Indies
| | - Firdous A. Khan
- Department of Large Animal Medicine and SurgerySchool of Veterinary MedicineSt. George's UniversityGrenadaWest Indies
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Doan T, Liu Z, Sié A, Dah C, Bountogo M, Ouattara M, Coulibaly B, Kiemde D, Zonou G, Nebie E, Brogdon J, Lebas E, Hinterwirth A, Zhong L, Chen C, Zhou Z, Porco T, Arnold BF, Oldenburg CE, Lietman TM. Gut Microbiome Diversity and Antimicrobial Resistance After a Single Dose of Oral Azithromycin in Children: A Randomized Placebo-Controlled Trial. Am J Trop Med Hyg 2024; 110:291-294. [PMID: 38227963 PMCID: PMC10859792 DOI: 10.4269/ajtmh.23-0651] [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: 09/18/2023] [Accepted: 10/25/2023] [Indexed: 01/18/2024] Open
Abstract
Mass antibiotic distribution to preschool children resulted in alterations of the gut microbiome months after distribution. This individually randomized, placebo-controlled trial evaluated changes in the gut microbiome and resistome in children aged 8 days to 59 months after one dose of oral azithromycin in Burkina Faso. A total of 450 children were randomized in a 1:1 ratio to either placebo or azithromycin. Rectal samples were collected at baseline, 2 weeks, and 6 months after randomization and subjected to DNA deep sequencing. Gut microbiome diversity and normalized antimicrobial resistance determinants for different antibiotic classes were evaluated. Azithromycin decreased gut bacterial diversity (Shannon P < 0.0001; inverse Simpson P < 0.001) 2 weeks after treatment relative to placebo. Concurrently, the normalized abundance of macrolide resistance genetic determinants was 243-fold higher (95% CI: 76-fold to 776-fold, P < 0.0001). These alterations did not persist at 6 months, suggesting that disruptions were transient. Furthermore, we were unable to detect resistance changes in other antibiotic classes, indicating that co-resistance with a single course of azithromycin when treated at the individual level was unlikely.
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Affiliation(s)
- Thuy Doan
- Francis I. Proctor Foundation, University of California, San Francisco, California
- Department of Ophthalmology, University of California, San Francisco, California
| | - Zijun Liu
- Department of Ophthalmology, University of California, San Francisco, California
| | - Ali Sié
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | - Clarisse Dah
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | | | | | | | - Dramane Kiemde
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | | | - Eric Nebie
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | - Jessica Brogdon
- Francis I. Proctor Foundation, University of California, San Francisco, California
| | - Elodie Lebas
- Francis I. Proctor Foundation, University of California, San Francisco, California
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California, San Francisco, California
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California, San Francisco, California
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California, San Francisco, California
| | - Zhaoxia Zhou
- Francis I. Proctor Foundation, University of California, San Francisco, California
| | - Travis Porco
- Francis I. Proctor Foundation, University of California, San Francisco, California
- Department of Ophthalmology, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - Benjamin F. Arnold
- Francis I. Proctor Foundation, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - Catherine E. Oldenburg
- Francis I. Proctor Foundation, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
- Institute for Global Health Sciences, University of California, San Francisco, California
| | - Thomas M. Lietman
- Francis I. Proctor Foundation, University of California, San Francisco, California
- Department of Ophthalmology, University of California, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
- Institute for Global Health Sciences, University of California, San Francisco, California
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Gafarova E, Kuracji D, Sogomonyan K, Gorokhov I, Polev D, Zubova E, Golikova E, Granovitch A, Maltseva A. Gut Bacteriomes and Ecological Niche Divergence: An Example of Two Cryptic Gastropod Species. BIOLOGY 2023; 12:1521. [PMID: 38132347 PMCID: PMC10740740 DOI: 10.3390/biology12121521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Symbiotic microorganisms may provide their hosts with abilities critical to their occupation of microhabitats. Gut (intestinal) bacterial communities aid animals to digest substrates that are either innutritious or toxic, as well as support their development and physiology. The role of microbial communities associated with sibling species in the hosts' adaptation remains largely unexplored. In this study, we examined the composition and plasticity of the bacteriomes in two sibling intertidal gastropod species, Littorina fabalis and L. obtusata, which are sympatric but differ in microhabitats. We applied 16S rRNA gene metabarcoding and shotgun sequencing to describe associated microbial communities and their spatial and temporal variation. A significant drop in the intestinal bacteriome diversity was revealed during the cold season, which may reflect temperature-related metabolic shifts and changes in snail behavior. Importantly, there were significant interspecies differences in the gut bacteriome composition in summer but not in autumn. The genera Vibrio, Aliivibrio, Moritella and Planktotalea were found to be predominantly associated with L. fabalis, while Granulosicoccus, Octadecabacter, Colwellia, Pseudomonas, Pseudoalteromonas and Maribacter were found to be mostly associated with L. obtusata. Based on these preferential associations, we analyzed the metabolic pathways' enrichment. We hypothesized that the L. obtusata gut bacteriome contributes to decomposing algae and detoxifying polyphenols produced by fucoids. Thus, differences in the sets of associated bacteria may equip their closely phylogenetically related hosts with a unique ability to occupy specific micro-niches.
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Affiliation(s)
- Elizaveta Gafarova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Kuracji
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Karina Sogomonyan
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ivan Gorokhov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Polev
- Department of Epidemiology, St. Petersburg Pasteur Institute, Mira Street 14, 197101 St. Petersburg, Russia;
| | - Ekaterina Zubova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Elena Golikova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Andrey Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Arina Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
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Medeot DB, Nilson A, Miazzo RD, Grosso V, Ferrari W, Jofré E, Soltermann A, Peralta MF. Stevia as a natural additive on gut health and cecal microbiota in broilers. Vet Anim Sci 2023; 22:100322. [PMID: 38045012 PMCID: PMC10692954 DOI: 10.1016/j.vas.2023.100322] [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] [Indexed: 12/05/2023] Open
Abstract
Stevia mash (SM), leaves of Stevia rebaudiana Bertoni plant, is an additive used in poultry that enhances growth and health. Objective: to determine the effect of 1 % SM on productive parameters, gut health, and the cecal microbiome in broilers between the first 15 and 21 days old. One hundred sixty male, 1-day-old broilers (48.5 ± 2.5 g) were divided into Control (C) without SM and Treated (T) with 1 % SM on diet, during 15/21 days. Each subgroup had eight broilers/five repetitions/treatment. At day 15 or 21, all broilers were dissected, Fabricius Bursa and Gut removed and processed for histomorphometry, followed by Villi Height/Crypt Deep (VH/CD) ratio. Conversion Index (CI) was determined. The V3-V4 region of 16S rRNA gene was amplified from DNA obtained from pooled cecal contents and sequenced on Illumina Miseq PE 2 × 250 platform. Sequence processing and taxonomic assignments were performed using the SHAMAN pipeline. Both T groups have better VH/CD Ratios than C groups (p ≤ 0.05). In guts, increased plasmatic and goblet cells number and thicker mucus layer were found in T15 and T21. All groups received SM showed early immunological maturity in Fabricius Bursa. IC was similar between all treatments. Faecalibacterium, Ruminococcus torques group, and Bacteroides were the major genera modulated by SM addition. At 15 and 21 days old, SM exerts a impact on diversity and evenness of the cecal microbiome. Conclusion: SM (1 %) produced early immunologic maturity on Fabricius Bursa, increased intestinal functionality, and modified the microbiota, increasing beneficial microbial genera and microbial diversity.
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Affiliation(s)
- Daniela B. Medeot
- Laboratorio de Biología Molecular de las Interacciones Planta-Bacteria-Instituto de Biotecnología Ambiental y de Salud (INBIAS)- Universidad Nacional de Rio Cuarto (UNRC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UNRC: ruta 36 Km 601-5800-Rio Cuarto, Córdoba, Argentina
| | - Armando Nilson
- Unidad de Investigación Aviar, Producción Avícola, Facultad de Agronomía y Veterinaria-UNRC, Argentina
| | - Raul D. Miazzo
- Unidad de Investigación Aviar, Producción Avícola, Facultad de Agronomía y Veterinaria-UNRC, Argentina
| | - Viviana Grosso
- Laboratorio de Vinculación Tecnológica, Facultad de Ciencias Exactas, Físico-Químicas y Naturales-UNRC, Argentina
| | - Walter Ferrari
- Laboratorio de Biología Molecular de las Interacciones Planta-Bacteria-Instituto de Biotecnología Ambiental y de Salud (INBIAS)- Universidad Nacional de Rio Cuarto (UNRC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UNRC: ruta 36 Km 601-5800-Rio Cuarto, Córdoba, Argentina
| | - Edgardo Jofré
- Laboratorio de Biología Molecular de las Interacciones Planta-Bacteria-Instituto de Biotecnología Ambiental y de Salud (INBIAS)- Universidad Nacional de Rio Cuarto (UNRC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) UNRC: ruta 36 Km 601-5800-Rio Cuarto, Córdoba, Argentina
| | - Arnaldo Soltermann
- Laboratorio de Vinculación Tecnológica, Facultad de Ciencias Exactas, Físico-Químicas y Naturales-UNRC, Argentina
| | - María Fernanda Peralta
- Unidad de Investigación Aviar, Producción Avícola, Facultad de Agronomía y Veterinaria-UNRC, Argentina
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8
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do Almo MM, Sousa IG, Olinto VG, Pinhate SB, Jivago JLDPR, de Sousa DER, de Castro MB, Rubini MR, Maranhão AQ, Brigido MM. Therapeutic Effects of Zymomonas mobilis on Experimental DSS-Induced Colitis Mouse Model. Microorganisms 2023; 11:2793. [PMID: 38004805 PMCID: PMC10672878 DOI: 10.3390/microorganisms11112793] [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: 10/16/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Zymomonas mobilis, a Gram-negative bacteria observed in some popular beverages, is considered safe and has been studied for its potential therapeutic benefits. In this study, we explored its effects on the inflammatory process, tissue integrity, differential gene expression, and microbiota composition in an experimental dextran sulfate sodium (DSS)-induced colitis model in mice. As a result, Z. mobilis alleviated the symptoms caused by DSS administration, as indicated by reduced weight loss, disease activity index, a significant reduction in the colon weight/length ratio, and histopathological improvement. Also, Z. mobilis could restore the mucosal barrier as well as increase the expression of Muc3 and Ocln genes. An analysis of 16S rRNA sequences showed that Z. mobilis alters gut microbiota, increasing Akkermansia muciniphila abundance and decreasing Escherichia coli. Furthermore, Z. mobilis seems to be involved in potentiating a regulatory phenotype by inducing immunomodulatory genes like Tgfb, Il5, Il10, and Foxp3 and reducing the relative mRNA expression of proinflammatory cytokines TNF, Il6, and Il17. Our data suggest that Z. mobilis could alleviate disease progression and be considered a possible probiotic adjuvant for pathologies of the bowel.
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Affiliation(s)
- Manuela Maragno do Almo
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (M.M.d.A.); (I.G.S.); (V.G.O.); (S.B.P.); (A.Q.M.)
- Molecular Pathology Graduation Program, Medicine Faculty, University of Brasilia, Brasilia 70910-900, Brazil
| | - Isabel Garcia Sousa
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (M.M.d.A.); (I.G.S.); (V.G.O.); (S.B.P.); (A.Q.M.)
| | - Vitor Guimarães Olinto
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (M.M.d.A.); (I.G.S.); (V.G.O.); (S.B.P.); (A.Q.M.)
- Molecular Biology Graduation Program, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | - Sylvia Barbosa Pinhate
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (M.M.d.A.); (I.G.S.); (V.G.O.); (S.B.P.); (A.Q.M.)
- Molecular Biology Graduation Program, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | | | - Davi Emanuel Ribeiro de Sousa
- Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasilia, Brasilia 70910-900, Brazil; (D.E.R.d.S.); (M.B.d.C.)
| | - Márcio Botelho de Castro
- Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasilia, Brasilia 70910-900, Brazil; (D.E.R.d.S.); (M.B.d.C.)
| | - Marciano Régis Rubini
- Laboratory of Genetics and Molecular Biology, Embrapa Agroenergy, Brasilia 70770-901, Brazil;
| | - Andrea Queiroz Maranhão
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (M.M.d.A.); (I.G.S.); (V.G.O.); (S.B.P.); (A.Q.M.)
- Institute for Immunology Investigation, National Institute of Science and Technology (iii-INCT), Brasilia 70067-900, Brazil
| | - Marcelo Macedo Brigido
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (M.M.d.A.); (I.G.S.); (V.G.O.); (S.B.P.); (A.Q.M.)
- Institute for Immunology Investigation, National Institute of Science and Technology (iii-INCT), Brasilia 70067-900, Brazil
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9
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Boopathi S, Meenatchi R, Brindangnanam P, Sudhakaran G, Coumar MS, Arockiaraj J. Microbiome analysis of Litopenaeus vannamei reveals Vibrio as main risk factor of white faeces syndrome. AQUACULTURE 2023; 576:739829. [DOI: 10.1016/j.aquaculture.2023.739829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
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10
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Angthong P, Chaiyapechara S, Rungrassamee W. Shrimp microbiome and immune development in the early life stages. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104765. [PMID: 37380117 DOI: 10.1016/j.dci.2023.104765] [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: 04/01/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
With its contribution to nutrition, development, and disease resistance, gut microbiome has been recognized as a crucial component of the animal's health and well-being. Microbiome in the gastrointestinal tract constantly interacts with the host animal's immune systems as part of the normal function of the intestines. Interactions between the microbiome and the immune system are complex and dynamic, with the microbiome shaping immune development and function. In contrast, the immune system modulates the composition and activity of the microbiome. In shrimp, as with all other aquatic animals, the interaction between the microbiome and the animals occurs at the early developmental stages. This early interaction is likely essential to the development of immune responses of the animal as well as many key physiological developments that further contribute to the health of shrimp. This review provides background knowledge on the early developmental stage of shrimp and its microbiome, examines the interaction between the microbiome and the immune system in the early life stage of shrimp, and discusses potential pitfalls and challenges associated with microbiome research. Understanding the interaction between the microbiome and shrimp immune system at this crucial developmental stage could have the potential to aid in the establishment of a healthy microbiome, improve shrimp survival, and provide ways to shape the microbiome with feed supplements or other strategies.
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Affiliation(s)
- Pacharaporn Angthong
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sage Chaiyapechara
- Aquaculture Service Development Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand.
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11
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Pheeha SM, Tamuzi JL, Chale-Matsau B, Manda S, Nyasulu PS. A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa. Microorganisms 2023; 11:2118. [PMID: 37630678 PMCID: PMC10458939 DOI: 10.3390/microorganisms11082118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations.
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Affiliation(s)
- Sara M. Pheeha
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Department of Chemical Pathology, Faculty of Medicine and Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- National Health Laboratory Service, Dr George Mukhari Academic Hospital, Pretoria 0208, South Africa
| | - Jacques L. Tamuzi
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
| | - Bettina Chale-Matsau
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa
- National Health Laboratory Service, Steve Biko Academic Hospital, Pretoria 0002, South Africa
| | - Samuel Manda
- Department of Statistics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
| | - Peter S. Nyasulu
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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12
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Guo M, Wu J, Hung W, Sun Z, Zhao W, Lan H, Zhao Z, Wuri G, Fang B, Zhao L, Zhang M. Lactobacillus paracasei ET-22 Suppresses Dental Caries by Regulating Microbiota of Dental Plaques and Inhibiting Biofilm Formation. Nutrients 2023; 15:3316. [PMID: 37571254 PMCID: PMC10421449 DOI: 10.3390/nu15153316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Dental caries is a common and multifactorial biofilm disease that is associated with dietary habits and microbiota. Among the various pathogens inducing caries, S. mutans is the most extensively studied. Promoting oral health with probiotics has gained considerable attention. Lactobacillus paracasei (L. paracasei) strains were reported to modulate the gut microbiota and enhance host resistance to disease. Our previous research has found that L. paracasei ET-22 (ET-22) could inhibit S. mutans biofilms in vitro. However, the preventive effect in vivo and functional mechanism of ET-22 on dental caries were unclear. In this study, the preventive effects of ET-22 on dental caries in mice were checked. Meanwhile, the functional mechanism of ET-22 was further investigated. Results showed that the supplementation of ET-22 in drinking water significantly improved the caries scoring of mice. The microbiota of dental plaques revealed that the live and heat-killed ET-22 similarly regulated the microbial structure in plaque biofilms. Functional prediction of PICRUSt showed that the addition of live and heat-killed ET-22 may inhibit biofilm formation. By the in vitro trials, the live and heat-killed ET-22 indeed inhibited the construction of S. mutans biofilms and EPS productions of biofilms. This evidence suggests that ET-22 can restrain dental caries by regulating the microbiota of dental plaques and inhibiting biofilm formation, which may be partly mediated by the body components of ET-22.
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Affiliation(s)
- Meng Guo
- School of Food and Health, Beijing Technology and Business University, Beijing 100024, China; (M.G.)
| | - Jianmin Wu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Weilian Hung
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China
| | - Zhe Sun
- School of Food and Health, Beijing Technology and Business University, Beijing 100024, China; (M.G.)
| | - Wen Zhao
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China
- National Center of Technology Innovation for Dairy, Hohhot 010110, China
| | - Hanglian Lan
- National Center of Technology Innovation for Dairy, Hohhot 010110, China
| | - Zhi Zhao
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Guna Wuri
- School of Food and Health, Beijing Technology and Business University, Beijing 100024, China; (M.G.)
| | - Bing Fang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Liang Zhao
- Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Laboratory of Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ming Zhang
- School of Food and Health, Beijing Technology and Business University, Beijing 100024, China; (M.G.)
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13
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Alemany I, Pérez-Cembranos A, Pérez-Mellado V, Castro JA, Picornell A, Ramon C, Jurado-Rivera JA. Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands. MICROBIAL ECOLOGY 2023; 85:1564-1577. [PMID: 35482107 PMCID: PMC10167182 DOI: 10.1007/s00248-022-02019-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/19/2022] [Indexed: 05/10/2023]
Abstract
Gut microbial communities provide essential functions to their hosts and are known to influence both their ecology and evolution. However, our knowledge of these complex associations is still very limited in reptiles. Here we report the 16S rRNA gene faecal microbiota profiles of two lizard species endemic to the Balearic archipelago (Podarcis lilfordi and P. pityusensis), encompassing their allopatric range of distribution through a noninvasive sampling, as an alternative to previous studies that implied killing specimens of these IUCN endangered and near-threatened species, respectively. Both lizard species showed a faecal microbiome composition consistent with their omnivorous trophic ecology, with a high representation of cellulolytic bacteria taxa. We also identified species-specific core microbiota signatures and retrieved lizard species, islet ascription, and seasonality as the main factors in explaining bacterial community composition. The different Balearic Podarcis populations are characterised by harbouring a high proportion of unique bacterial taxa, thus reinforcing their view as unique and divergent evolutionary entities.
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Affiliation(s)
- Iris Alemany
- Department of Biology, University of the Balearic Islands, Ctra., Valldemossa km 7'5, 07122, Palma, Balearic Islands, Spain
| | | | | | - José A Castro
- Department of Biology, University of the Balearic Islands, Ctra., Valldemossa km 7'5, 07122, Palma, Balearic Islands, Spain
| | - Antonia Picornell
- Department of Biology, University of the Balearic Islands, Ctra., Valldemossa km 7'5, 07122, Palma, Balearic Islands, Spain
| | - Cori Ramon
- Department of Biology, University of the Balearic Islands, Ctra., Valldemossa km 7'5, 07122, Palma, Balearic Islands, Spain
| | - José A Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra., Valldemossa km 7'5, 07122, Palma, Balearic Islands, Spain.
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14
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Banjong D, Pongking T, Tran NTD, Pinlaor S, Dangtakot R, Intuyod K, Anutrakulchai S, Cha’on U, Pinlaor P. Slight Changes in the Gut Microbiome in Early-stage Chronic Kidney Disease of Unknown Etiology. Microbes Environ 2023; 38:ME22097. [PMID: 37635077 PMCID: PMC10522841 DOI: 10.1264/jsme2.me22097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/23/2023] [Indexed: 08/29/2023] Open
Abstract
Gut dysbiosis and changes in short-chain fatty acids (SCFAs) occur in end-stage chronic kidney disease (CKD); however, the degree of these changes in the gut microbiome and serum SCFA profiles in the early stages of CKD, particularly in CKD of unknown etiology (CKDu), is unclear. We herein investigated the gut microbiome and SCFA profiles of early-stage CKD patients (CKD stages 1-3) in a community in Khon Kaen Province, Thailand. Seventy-two parasite-free participants were distributed among a healthy control group (HC, n=18) and three patient groups (an underlying disease group [UD, n=18], early-stage CKD with underlying disease [CKD-UD, n=18], and early-stage CKD of unknown etiology, [CKDu, n=18]). Fecal DNA was individually extracted and pooled for groups of six individuals (three pools in each group) to examine the composition of the gut microbiome using next-generation sequencing. A SCFA ana-lysis was performed on serum samples from each individual using gas chromatography-mass spectrometry. The results revealed that microbial abundance differed between the healthy group and all patient groups (UD, CKD-UD, and CKDu). [Eubacterium]_coprostanoligenes_group was more abundant in the CKDu group than in the HC and CKD-UD groups. Furthermore, serum concentrations of acetate, a major SCFA component, were significantly lower in all patient groups than in the HC group. The present results indicate that minor changes in the gut microbiome and a significant decrease in serum acetate concentrations occur in early-stage CKDu, which may be important for the development of prevention strategies for CKD patients.
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Affiliation(s)
- Ditsayathan Banjong
- Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Thatsanapong Pongking
- Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Na T. D. Tran
- Faculty of Medical Laboratory Science, Danang University of Medical Technology and Pharmacy, Danang, Vietnam
| | - Somchai Pinlaor
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Rungtiwa Dangtakot
- Faculty of Medical Technology, Nakhonratchasima College, Nakhon Ratchasima, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Kitti Intuyod
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Sirirat Anutrakulchai
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Ubon Cha’on
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
| | - Porntip Pinlaor
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen, Thailand
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15
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Dong H, Chen X, Zhao X, Zhao C, Mehmood K, Kulyar MFEA, Bhutta ZA, Zeng J, Nawaz S, Wu Q, Li K. Intestine microbiota and SCFAs response in naturally Cryptosporidium-infected plateau yaks. Front Cell Infect Microbiol 2023; 13:1105126. [PMID: 36936759 PMCID: PMC10014559 DOI: 10.3389/fcimb.2023.1105126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Diarrhea is a severe bovine disease, globally prevalent in farm animals with a decrease in milk production and a low fertility rate. Cryptosporidium spp. are important zoonotic agents of bovine diarrhea. However, little is known about microbiota and short-chain fatty acids (SCFAs) changes in yaks infected with Cryptosporidium spp. Therefore, we performed 16S rRNA sequencing and detected the concentrations of SCFAs in Cryptosporidium-infected yaks. Results showed that over 80,000 raw and 70,000 filtered sequences were prevalent in yak samples. Shannon (p<0.01) and Simpson (p<0.01) were both significantly higher in Cryptosporidium-infected yaks. A total of 1072 amplicon sequence variants were shared in healthy and infected yaks. There were 11 phyla and 58 genera that differ significantly between the two yak groups. A total of 235 enzymes with a significant difference in abundance (p<0.001) were found between healthy and infected yaks. KEGG L3 analysis discovered that the abundance of 43 pathways was significantly higher, while 49 pathways were significantly lower in Cryptosporidium-infected yaks. The concentration of acetic acid (p<0.05), propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05), and isovaleric acid was noticeably lower in infected yaks, respectively. The findings of the study revealed that Cryptosporidium infection causes gut dysbiosis and results in a significant drop in the SCFAs concentrations in yaks with severe diarrhea, which may give new insights regarding the prevention and treatment of diarrhea in livestock.
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Affiliation(s)
- Hailong Dong
- Key Laboratory of Clinical Veterinary Medicine in Tibet, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Xiushuang Chen
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiao Zhao
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chenxi Zhao
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Khalid Mehmood
- Department of Clinical Medicine and Surgery, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Jiangyong Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Shah Nawaz
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Qingxia Wu
- Key Laboratory of Clinical Veterinary Medicine in Tibet, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- *Correspondence: Qingxia Wu, ; Kun Li,
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Qingxia Wu, ; Kun Li,
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16
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Deng Y, Chen H, Huang Y, Zhang Y, Ren H, Fang M, Wang Q, Chen W, Hale RC, Galloway TS, Chen D. Long-Term Exposure to Environmentally Relevant Doses of Large Polystyrene Microplastics Disturbs Lipid Homeostasis via Bowel Function Interference. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15805-15817. [PMID: 36282942 DOI: 10.1021/acs.est.1c07933] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The question of whether long-term chronic exposure to microplastics (MPs) could induce dose- and size-dependent adverse effects in mammals remains controversial and poorly understood. Our study explored potential health risks from dietary exposure to environmentally relevant doses of polystyrene (PS) MPs, through a mouse model and integrated analyses of the interruptions of fecal microbial metagenomes and plasma lipidomes. After 21 weeks of exposure to the MPs (40-100 μm), mice mainly exhibited gut microbiota dysbiosis, tissue inflammation, and plasma lipid metabolism disorder, although no notable accumulation of MPs was observed in the gut or liver. The change of the relative abundance of microbiota was strongly associated with the exposure dose and size of MPs while less significant effects were observed in gut damage and abnormal lipid metabolism. Moreover, multiomics data suggested that the host abnormal lipid metabolism was closely related to bowel function disruptions, including gut microbiota dysbiosis, increased gut permeability, and inflammation induced by MPs. We revealed for the first time that even without notable accumulation in mouse tissues, long-term exposure to MPs at environmentally relevant doses could still induce widespread health risks. This raises concern on the health risks from the exposure of humans and other mammals to environmentally relevant dose MPs.
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Affiliation(s)
- Yongfeng Deng
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Hexia Chen
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Yichao Huang
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Qing Wang
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Robert C Hale
- Virginia Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, Virginia 23062, United States
| | - Tamara S Galloway
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, United Kingdom
| | - Da Chen
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
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17
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Kharnaior P, Tamang JP. Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas. Front Microbiol 2022; 13:868383. [PMID: 35572705 PMCID: PMC9106393 DOI: 10.3389/fmicb.2022.868383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/24/2022] [Indexed: 12/18/2022] Open
Abstract
Kinema is a popular sticky fermented soybean food of the Eastern Himalayan regions of North East India, east Nepal, and south Bhutan. We hypothesized that some dominant bacteria in kinema may contribute to the formation of targeted and non-targeted metabolites for health benefits; hence, we studied the microbiome-metabolite mining of kinema. A total of 1,394,094,912 bp with an average of 464,698,304 ± 120,720,392 bp was generated from kinema metagenome, which resulted in the identification of 47 phyla, 331 families, 709 genera, and 1,560 species. Bacteria (97.78%) were the most abundant domain with the remaining domains of viruses, eukaryote, and archaea. Firmicutes (93.36%) was the most abundant phylum with 280 species of Bacillus, among which Bacillus subtilis was the most dominant species in kinema followed by B. glycinifermentans, B. cereus, B. licheniformis, B. thermoamylovorans, B. coagulans, B. circulans, B. paralicheniformis, and Brevibacillus borstelensis. Predictive metabolic pathways revealed the abundance of genes associated with metabolism (60.66%), resulting in 216 sub-pathways. A total of 361 metabolites were identified by metabolomic analysis (liquid chromatography-mass spectrophotometry, LC-MS). The presence of metabolites, such as chrysin, swainsonine, and 3-hydroxy-L-kynurenine (anticancer activity) and benzimidazole (antimicrobial, anticancer, and anti-HIV activities), and compounds with immunomodulatory effects in kinema supports its therapeutic potential. The correlation between the abundant species of Bacillus and primary and secondary metabolites was constructed with a bivariate result. This study proves that Bacillus spp. contribute to the formation of many targeted and untargeted metabolites in kinema for health-promoting benefits.
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Affiliation(s)
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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18
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Sonalio K, Almeida HMS, Mechler-Dreibi ML, Storino GY, Haesebrouck F, Maes D, de Oliveira LG. Influence of Mycoplasma hyopneumoniae natural infection on the respiratory microbiome diversity of finishing pigs. Vet Res 2022; 53:20. [PMID: 35303928 PMCID: PMC8932171 DOI: 10.1186/s13567-022-01038-9] [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: 11/27/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
Mycoplasma (M.) hyopneumoniae interacts with the respiratory microbiota and facilitates colonization of other pathogens. The present study investigated the pulmonary and nasal microbiota of M. hyopneumoniae-infected and M. hyopneumoniae-free pigs. Sixty-six pigs from three commercial herds were selected at the end of the finishing phase: 44 originated from two M. hyopneumoniae-positive herds and 22 from a M. hyopneumoniae-negative farm. At the slaughterhouse, samples of nasal turbinate (NT) and bronchus-alveolar lavage fluid (BALF) were collected. DNA was extracted with a commercial kit and the infection status was confirmed by qPCR. All samples from the same herd were pooled, and next-generation sequencing based on the hypervariable region V3-V4 of the 16 s bacterial rDNA was performed. Data analysis included the taxonomic analysis, Alpha diversity indexes, and Principal coordinates analysis (Pcoa) using Jaccard, Bray-Curtis, Weighted Unifrac, and Unweighted Unifrac distances. All pigs from the infected herds tested PCR positive for M. hyopneumoniae, whereas all pigs from the negative farm were negative. There was a greater diversity of microorganisms in BALF when compared to NT samples in all the farms. BALF samples from infected animals showed higher abundance of M. hyopneumoniae than NT samples and a predominance of Pasteurella multocida among the main species identified, which was also abundant in the M. hyopneumoniae-free herd. PCoa diagrams indicated that for most of the samples, dissimilarity on bacterial composition was observed, regardless of infection status and sample type. Therefore, the lung microbiota was modulated by M. hyopneumoniae infection, which could play a role in the pathogenesis of M. hyopneumoniae-disease.
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Affiliation(s)
- Karina Sonalio
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.,Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Henrique M S Almeida
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Marina L Mechler-Dreibi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Gabriel Y Storino
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | - Dominiek Maes
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Luís Guilherme de Oliveira
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.
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19
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NGUYEN HT, HONGSRICHAN N, INTUYOD K, PINLAOR P, YINGKLANG M, CHAIDEE A, SENGTHONG C, PONGKING T, DANGTAKOT R, BANJONG D, ANUTRAKULCHAI S, CHA’ON U, PINLAOR S. Investigation of gut microbiota and short-chain fatty acids in <i>Strongyloides stercoralis</i>-infected patients in a rural community. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2022; 41:121-129. [PMID: 35854692 PMCID: PMC9246423 DOI: 10.12938/bmfh.2021-054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/05/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Hai Thi NGUYEN
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nuttanan HONGSRICHAN
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kitti INTUYOD
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Porntip PINLAOR
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Manachai YINGKLANG
- Department of Fundamentals of Public Health, Faculty of Public Health, Burapha University, Chonburi 20131, Thailand
| | - Apisit CHAIDEE
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chatchawan SENGTHONG
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thatsanapong PONGKING
- Science Program in Biomedical Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Rungthiwa DANGTAKOT
- Department of Medical Technology, Faculty of Allied Health Sciences, Nakhonratchasima college, Nakhon Ratchasima, 30000, Thailand
| | - Ditsayathan BANJONG
- Science Program in Biomedical Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sirirat ANUTRAKULCHAI
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Ubon CHA’ON
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Somchai PINLAOR
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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Tamang JP, Das S, Kharnaior P, Pariyar P, Thapa N, Jo SW, Yim EJ, Shin DH. Shotgun metagenomics of Cheonggukjang, a fermented soybean food of Korea: Community structure, predictive functionalities and amino acids profile. Food Res Int 2022; 151:110904. [PMID: 34980421 DOI: 10.1016/j.foodres.2021.110904] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 09/10/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022]
Abstract
Cheonggukjang is a naturally fermented soybean food of Korea. The present study was aimed to reveal the whole microbial community structure of naturally fermented cheonggukjang along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. Metataxonomic profile of cheonggukjang samples showed different domains viz. bacteria (95.83%), virus (2.26%), unclassified (1.84%), eukaryotes (0.05%) and archaea (0.005%). Overall, 44 phyla, 286 families, 722 genera and 1437 species were identified. Firmicutes was the most abundant phylum (98.04%) followed by Proteobacteria (1.49%), Deinococcus-Thermus (0.14%). Bacillus thermoamylovorans was the most abundant species in cheonggukjang followed by Bacillus licheniformis, Bacillus glycinifermentans, Bacillus subtilis, Bacillus paralicheniformis, Bacillus amyloliquifaciens, Brevibacillus borstelensis, Brevibacillus sonorensis Brevibacillus, Acinetobacter, Carnobacterium, Paenibacillus, Cronobacter Enterococcus, Enterobacter, Terriglobus, Psychrobacter and Virgibacillus. A colossal diversity of the genus Bacillus was detected with 150 species. Functional analysis of cheonggukjang metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including, various essential amino acids, conjugated amino acids, different vitamins, flavonoids, and enzymes. Amino acid profiles obtained from KEGG annotation in cheonggukjang were validated with experimental result of amino acid profiles.
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Affiliation(s)
- Jyoti Prakash Tamang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India.
| | - Souvik Das
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Pynhunlang Kharnaior
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Priyambada Pariyar
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Namrata Thapa
- Biotech Hub, Department of Zoology, Nar Bahadur Bhandari Degree College, Sikkim University, Tadong 737102, Sikkim, India.
| | - Seung-Wha Jo
- Microbial Institute for Fermentation Industry (MIFI), Sunchang 56048, Republic of Korea
| | - Eun-Jung Yim
- Microbial Institute for Fermentation Industry (MIFI), Sunchang 56048, Republic of Korea
| | - Dong-Hwa Shin
- Shindonghwa Food Research Institute, Seoul 06192, Republic of Korea
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21
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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22
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Vasquez A, Nydam D, Foditsch C, Warnick L, Wolfe C, Doster E, Morley PS. Characterization and comparison of the microbiomes and resistomes of colostrum from selectively treated dry cows. J Dairy Sci 2021; 105:637-653. [PMID: 34763917 DOI: 10.3168/jds.2021-20675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022]
Abstract
Professionals in animal agriculture promote prudent use of antimicrobials to address public and animal health concerns, such as reduction of antimicrobial residues and antimicrobial resistance (AMR) in products. Few studies evaluate the effect of selective dry-cow therapy on preservation of the milk microbiome or the profile of AMR genes (the resistome) present at freshening. Our objectives were to characterize and compare the microbiomes and resistomes in the colostrum of cows with low somatic cell count that were treated or not treated with intramammary cephapirin benzathine at dry-off. From a larger parent study, cows on a New York dairy farm eligible for dry-off and with histories of somatic cell counts ≤200,000 cells/mL were enrolled to this study (n = 307). Cows were randomly assigned to receive an intramammary antimicrobial and external teat sealant (ABXTS) or sealant only (TS) at dry-off. Composite colostrum samples taken within 4 h of freshening, and quarter milk samples taken at 1 to 7 d in milk were subjected to aerobic culture. The DNA extraction was performed on colostrum from cows with culture-negative samples (ABXTS = 43; TS = 33). The DNA from cows of the same treatment group and parity were pooled (26 pools; ABXTS = 12; TS = 14) for 16S rRNA metagenomic sequencing. Separately, the resistome was captured using a custom RNA bait library for target-enriched sequencing. Sequencing reads were aligned to taxonomic and AMR databases to characterize the microbiome and resistome, respectively. The R statistical program was used to tabulate abundances and to analyze differences in diversity measures and in composition between treatment groups. In the microbiome, the most abundant phyla were Firmicutes (68%), Proteobacteria (23%), Actinobacteria (4%), and Bacteroidetes (3%). Shannon and richness diversity means were 0.93 and 14.7 for ABXTS and 0.94 and 13.1 for TS, respectively. Using analysis of similarities (ANOSIM), overall microbiome composition was found to be similar between treatment groups at the phylum (ANOSIM R = 0.005), class (ANOSIM R = 0.04), and order (ANOSIM R = -0.04) levels. In the resistome, we identified AMR gene accessions associated with 14 unique mechanisms of resistance across 9 different drug classes in 14 samples (TS = 9, ABXTS = 5). The majority of reads aligned to gene accessions that confer resistance to aminoglycoside (TS = ABXTS each 35% abundance), tetracycline (TS = 22%, ABXTS = 54%), and β-lactam classes (TS = 15%, ABXTS = 12%). Shannon diversity means for AMR class and mechanism, respectively, were 0.66 and 0.69 for TS and 0.19 and 0.19 for ABXTS. Resistome richness diversity means for class and mechanism were 3.1 and 3.4 for TS and 1.4 and 1.4 for ABXTS. Finally, resistome composition was similar between groups at the class (ANOSIM R = -0.20) and mechanism levels (ANOSIM R = 0.01). Although no critical differences were found between treatment groups regarding their microbiome or resistome composition in this study, a larger sample size, deeper sequencing, and additional methodology is needed to identify more subtle differences, such as between lower-abundance features.
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Affiliation(s)
- Amy Vasquez
- Department of Population Medicine, Cornell College of Veterinary Medicine, Ithaca, NY 14853.
| | - Daryl Nydam
- Department of Population Medicine, Cornell College of Veterinary Medicine, Ithaca, NY 14853
| | - Carla Foditsch
- Department of Population Medicine, Cornell College of Veterinary Medicine, Ithaca, NY 14853
| | - Lorin Warnick
- Department of Population Medicine, Cornell College of Veterinary Medicine, Ithaca, NY 14853
| | - Cory Wolfe
- Veterinary Education, Research, and Outreach Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon 79015
| | - Enrique Doster
- Veterinary Education, Research, and Outreach Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon 79015; Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins 80521
| | - Paul S Morley
- Veterinary Education, Research, and Outreach Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon 79015
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Chekanov K, Zaytseva A, Mamedov I, Solovchenko A, Lobakova E. The Dynamics of the Bacterial Community of the Photobioreactor-Cultivated Green Microalga Haematococcus lacustris during Stress-Induced Astaxanthin Accumulation. BIOLOGY 2021; 10:biology10020115. [PMID: 33557358 PMCID: PMC7915213 DOI: 10.3390/biology10020115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 12/02/2022]
Abstract
Simple Summary The microalga Haematococcus lacustris is a source of the natural colorant astaxanthin, a powerful antioxidant and key component of cosmetics and animal feed. Haematococcus is cultivated in photobioreactors. It can obtain energy just from a light illuminating photobioreactor and uses inorganic salts and CO2 as sources for chemical elements. The most widespread approach for Haematococcus cultivation is the two stage scheme. At the first stage, biomass accumulation under favorable growth conditions occurs. At the second stage, the cells are subjected to stress inducing astaxanthin synthesis. Generally, the culture of Haematococcus is not axenic. It exists in the form of a community with bacteria constituting its microbiome. The information on photobioreactor-cultivated Haematococcus microbiome is scarce. We analyzed its dynamic during astaxanthin production by DNA metabarcoding and microscopic observations. The main results of the work include the characterization of the daily dynamic of this microbiome and the revealing of contact between microalgae and bacteria. These findings are of potential significance for biotechnology. On one hand, they provide an insight into possible bacterial contamination of the harvested algal biomass. On the other hand, they reveal the presence of a core microbiome or bacteria essential for the growth of the microalga existing in all Haematococcus cultures. Abstract Haematococcus lacustris is a natural source of a valuable ketocarotenoid astaxanthin. Under autotrophic growth conditions, it exists in the form of a community with bacteria. The close coexistence of these microorganisms raises two questions: how broad their diversity is and how they interact with the microalga. Despite the importance these issues, little is known about microorganisms existing in Haematococcus cultures. For the first time, we characterize the dynamic of the H. lacustris microbiome of the microbiome of Haematococcus (a changeover of the bacterial associated species as function of the time) cultivated autotrophically in a photobioreactor based on 16S rRNA metabarcoding data. We found that Proteobacteria and Bacteroidetes are predominant phyla in the community. The Caulobacter bacterium became abundant during astaxanthin accumulation. These data were supported by microscopy. We discuss possible roles and interactions of the community members. These findings are of potential significance for biotechnology. They provide an insight into possible bacterial contamination in algal biomass and reveal the presence of bacteria essential for the algal growth.
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Affiliation(s)
- Konstantin Chekanov
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (A.Z.); (A.S.); (E.L.)
- Centre for Humanities Research and Technology, National Research Nuclear University MEPhI, 31 Kashirskoye Highway, 115522 Moscow, Russia
- Correspondence:
| | - Anna Zaytseva
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (A.Z.); (A.S.); (E.L.)
| | - Ilgar Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Alexei Solovchenko
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (A.Z.); (A.S.); (E.L.)
- Institute of Natural Sciences, Derzahvin Tambov State University, 39200 Tambov, Russia
| | - Elena Lobakova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (A.Z.); (A.S.); (E.L.)
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Doan T, Worden L, Hinterwirth A, Arzika AM, Maliki R, Abdou A, Zhong L, Chen C, Cook C, Lebas E, O’Brien KS, Oldenburg CE, Chow ED, Porco TC, Lipsitch M, Keenan JD, Lietman TM. Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution. N Engl J Med 2020; 383:1941-1950. [PMID: 33176084 PMCID: PMC7492079 DOI: 10.1056/nejmoa2002606] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mass distribution of azithromycin to preschool children twice yearly for 2 years has been shown to reduce childhood mortality in sub-Saharan Africa but at the cost of amplifying macrolide resistance. The effects on the gut resistome, a reservoir of antimicrobial resistance genes in the body, of twice-yearly administration of azithromycin for a longer period are unclear. METHODS We investigated the gut resistome of children after they received twice-yearly distributions of azithromycin for 4 years. In the Niger site of the MORDOR trial, we enrolled 30 villages in a concurrent trial in which they were randomly assigned to receive mass distribution of either azithromycin or placebo, offered to all children 1 to 59 months of age every 6 months for 4 years. Rectal swabs were collected at baseline, 36 months, and 48 months for analysis of the participants' gut resistome. The primary outcome was the ratio of macrolide-resistance determinants in the azithromycin group to those in the placebo group at 48 months. RESULTS Over the entire 48-month period, the mean (±SD) coverage was 86.6±12% in the villages that received placebo and 83.2±16.4% in the villages that received azithromycin. A total of 3232 samples were collected during the entire trial period; of the samples obtained at the 48-month monitoring visit, 546 samples from 15 villages that received placebo and 504 from 14 villages that received azithromycin were analyzed. Determinants of macrolide resistance were higher in the azithromycin group than in the placebo group: 7.4 times as high (95% confidence interval [CI], 4.0 to 16.7) at 36 months and 7.5 times as high (95% CI, 3.8 to 23.1) at 48 months. Continued mass azithromycin distributions also selected for determinants of nonmacrolide resistance, including resistance to beta-lactam antibiotics, an antibiotic class prescribed frequently in this region of Africa. CONCLUSIONS Among villages assigned to receive mass distributions of azithromycin or placebo twice yearly for 4 years, antibiotic resistance was more common in the villages that received azithromycin than in those that received placebo. This trial showed that mass azithromycin distributions may propagate antibiotic resistance. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov number, NCT02047981.).
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Affiliation(s)
- Thuy Doan
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
| | - Lee Worden
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Armin Hinterwirth
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | | | | | - Amza Abdou
- Ministry of Health, Niger
- Programme National de Santé Oculaire, Niger
| | - Lina Zhong
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Cindi Chen
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Catherine Cook
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Elodie Lebas
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Kieran S. O’Brien
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Catherine E. Oldenburg
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
| | - Eric D. Chow
- Department of Biochemistry and Biophysics, University of
California San Francisco, USA
| | - Travis C. Porco
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of
Public Health, Harvard University, MA, USA
| | - Jeremy D. Keenan
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
| | - Thomas M. Lietman
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
- Institute for Global Health Sciences, University of
California San Francisco, USA
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25
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Thinesh T, Meenatchi R, Lipton AN, Anandham R, Jose PA, Tang SL, Seghal Kiran G, Selvin J. Metagenomic sequencing reveals altered bacterial abundance during coral-sponge interaction: Insights into the invasive process of coral-killing sponge Terpios hoshinota. Microbiol Res 2020; 240:126553. [PMID: 32711340 DOI: 10.1016/j.micres.2020.126553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/26/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023]
Abstract
The coral-killing invasive sponge, Terpios hoshinota, causes extensive mortality to live corals and is a potential threat to reefs at different geographical locations. However, to date, the invasive mechanism remains largely unknown. In this study, we aimed to understand the bacterial competition between sponge and coral hosted bacteria when sponge outcompetes corals. We analysed the bacterial community of Terpios-invaded coral tissue, and the adjacent healthy tissue of sponge-invaded Favites colonies from Palk bay reef (South East Asia) of the Indian Ocean by using next-generation sequencing. Comparative analysis revealed similar bacterial diversity in both healthy and sponge covered coral tissues. However, relative abundance found to be differed between the groups. Terpios covered coral tissue had higher bacterial abundance than the healthy coral tissue. Bacterial phyla such as Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia live both in sponge covered and healthy coral tissue. Notably, many of the lower abundant bacteria in healthy coral tissue (abundance <1%) became the most abundant in sponge-invaded tissue. In particular, the genus Neisseria, Bacteroides, and members of Pseudoalteromonas predominant in sponge-invaded tissue. Similar bacterial diversity between normal and and sponge-invaded coral tissues suggest that bacteria follow an exploitative competition, which might favoured sponge growth over corals.
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Affiliation(s)
- T Thinesh
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - R Meenatchi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu 625 104, India
| | - Polpass Arul Jose
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu 625 104, India
| | - Sen-Lin Tang
- Biodiversity Research Centre, Academia sinica, Taiwan
| | - G Seghal Kiran
- Department of Food Science and Technology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
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26
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Actions of Trace Amines in the Brain-Gut-Microbiome Axis via Trace Amine-Associated Receptor-1 (TAAR1). Cell Mol Neurobiol 2019; 40:191-201. [DOI: 10.1007/s10571-019-00772-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022]
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27
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Zhang QL, Li HW, Wu W, Zhang M, Guo J, Deng XY, Wang F, Lin LB. The Response of Microbiota Community to Streptococcus agalactiae Infection in Zebrafish Intestine. Front Microbiol 2019; 10:2848. [PMID: 31866993 PMCID: PMC6908962 DOI: 10.3389/fmicb.2019.02848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022] Open
Abstract
Recently, Streptococcus agalactiae has become a major pathogen leading to Streptococcosis. To understand the physiological responses of zebrafish (Danio rerio) to S. agalactiae, the intestinal microbiota composition of the intestine (12 and 24 h post-infection, hpi, respectively) in zebrafish infected with S. agalactiae were investigated. The intestinal bacterial composition was analyzed using PacBio high-throughput full-length 16S rRNA gene sequencing. The most predominant bacteria in the zebrafish intestine were the Fusobacteria phylum and Sphingomonas genus. S. agalactiae infection affected the composition of partially intestinal microbiota. At the species level, the relative abundance of the pathogenic intestinal bacteria Aeromonas veronii, S. agalactiae, and Clostridium tarantellae significantly increased after S. agalactiae infection (p < 0.05), while that of the beneficial intestinal bacteria Bacillus licheniformis, Comamonas koreensis, and Romboutsia ilealis significantly decreased (p < 0.05), showing that S. agalactiae infection aggravates the zebrafish disease through promoting abundance of other intestinal pathogenic bacteria. This study is the first PacBio analyses of the zebrafish intestinal microbiota community under pathogenic infection. Results suggest that the S. agalactiae infection alters the intestinal flora structure in zebrafish.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Wei Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Man Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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