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Maslennikov R, Ivashkin V, Efremova I, Poluektova E, Kudryavtseva A, Krasnov G. Gut dysbiosis and small intestinal bacterial overgrowth as independent forms of gut microbiota disorders in cirrhosis. World J Gastroenterol 2022; 28:1067-1077. [PMID: 35431497 PMCID: PMC8968519 DOI: 10.3748/wjg.v28.i10.1067] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/29/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut dysbiosis and small intestinal bacterial overgrowth (SIBO) are commonly observed in patients with cirrhosis. Despite the substantial number of articles describing the relations between disorders of gut microbiota and various manifestations of cirrhosis, dysbiosis and SIBO were always studied separately.
AIM To study the relationship of gut dysbiosis and SIBO in cirrhosis.
METHODS This observational study included 47 in-patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. SIBO was assessed using the lactulose hydrogen breath test.
RESULTS SIBO was found in 24/47 (51.1%) patients. Patients with SIBO had a higher abundance of Firmicutes (P = 0.017) and Fusobacteria (P = 0.011), and a lower abundance of Bacteroidetes (P = 0.013) than patients without SIBO. This increase in the abundance of Firmicutes occurred mainly due to an increase in the abundance of bacteria from the genus Blautia (P = 0.020) of the Lachnospiraceae family (P = 0.047), while the abundance of other major families of this phylum [Ruminococcaceae (P = 0.856), Peptostreptococcaceae (P = 0.066), Clostridiaceae (P = 0.463), Eubacteriaceae (P = 0.463), Lactobacillaceae (P = 0.413), and Veillonellaceae (P = 0.632)] did not differ significantly between the patients with and without SIBO. Reduced level of Bacteroidetes in samples from patients with SIBO was a result of the decrease in bacterial numbers from all the major families of this phylum [Bacteroidaceae (P = 0.014), Porphyromonadaceae (P = 0.002), and Rikenellaceae (P = 0.047)], with the exception of Prevotellaceae (P = 0.941). There were no significant differences in the abundance of taxa that were the main biomarkers of cirrhosis-associated gut dysbiosis [Proteobacteria (P = 0.790), Bacilli (P = 0.573), Enterobacteriaceae (P = 0.632), Streptococcaceae (P = 0.170), Staphylococcaceae (P = 0.450), and Enterococcaceae (P = 0.873)] between patients with and without SIBO.
CONCLUSION Despite the differences observed in the gut microbiome between patients with and without SIBO, gut dysbiosis and SIBO are most likely independent disorders of gut microbiota in cirrhosis.
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Affiliation(s)
- Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Department of Internal Medicine 1, Сonsultative and Diagnostic Center 2 of the Moscow City Health Department, Moscow 107564, Russia
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Irina Efremova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Anna Kudryavtseva
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Brusilovsky M, Bao R, Rochman M, Kemter AM, Nagler CR, Rothenberg ME. Host-Microbiota Interactions in the Esophagus During Homeostasis and Allergic Inflammation. Gastroenterology 2022; 162:521-534.e8. [PMID: 34627858 PMCID: PMC9185752 DOI: 10.1053/j.gastro.2021.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/10/2021] [Accepted: 10/04/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND & AIMS Microbiota composition and mechanisms of host-microbiota interactions in the esophagus are unclear. We aimed to uncover fundamental information about the esophageal microbiome and its potential significance to eosinophilic esophagitis (EoE). METHODS Microbiota composition, transplantation potential, and antibiotic responsiveness in the esophagus were established via 16S ribosomal RNA sequencing. Functional outcomes of microbiota colonization were assessed by RNA sequencing analysis of mouse esophageal epithelium and compared with the human EoE transcriptome. The impact of dysbiosis was assessed using a preclinical model of EoE. RESULTS We found that the murine esophagus is colonized with diverse microbial communities within the first month of life. The esophageal microbiota is distinct, dominated by Lactobacillales, and demonstrates spatial heterogeneity as the proximal and distal esophagus are enriched in Bifidobacteriales and Lactobacillales, respectively. Fecal matter transplantation restores the esophageal microbiota, demonstrating that the local environment drives diversity. Microbiota colonization modifies esophageal tissue morphology and gene expression that is enriched in pathways associated with epithelial barrier function and overlapping with genes involved in EoE, including POSTN, KLK5, and HIF1A. Finally, neonatal antibiotic treatment reduces the abundance of Lactobacillales and exaggerates type 2 inflammation in the esophagus. Clinical data substantiated loss of esophageal Lactobacillales in EoE compared with controls. CONCLUSIONS The esophagus has a unique microbiome with notable differences between its proximal and distal regions. Fecal matter transplantation restores the esophageal microbiome. Antibiotic-induced dysbiosis exacerbates disease in a murine model of EoE. Collectively, these data establish the composition, transplantation potential, antibiotic responsiveness, and host-microbiota interaction in the esophagus and have implications for gastrointestinal health and disease.
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Affiliation(s)
- Michael Brusilovsky
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Riyue Bao
- Department of Pediatrics, University of Chicago, Chicago, Illinois; Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Andrea M Kemter
- Department of Pathology, Biological Sciences Division, University of Chicago, Chicago, Illinois
| | - Cathryn R Nagler
- Department of Pathology, Biological Sciences Division, University of Chicago, Chicago, Illinois; Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois.
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE. Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. Microbiol Spectr 2021; 9:e0178221. [PMID: 34908470 PMCID: PMC8672879 DOI: 10.1128/spectrum.01782-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Sidharth Rajesh
- Clements High School (Class of 2023), Fort Bend Independent School District, Sugar Land, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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Chen T, Ding R, Chen X, Lu Y, Shi J, Lü Y, Tang B, Zhang W, Ye C, Yuan M, Yang Z. Firmicutes and Blautia in gut microbiota lessened in chronic liver diseases and hepatocellular carcinoma patients: a pilot study. Bioengineered 2021; 12:8233-8246. [PMID: 34592890 PMCID: PMC8806631 DOI: 10.1080/21655979.2021.1982273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota system plays a vital role in liver diseases. This study aimed to address the diversity of gut microbiota and its correlations with clinical parameters in healthy individuals, chronic liver disease (CLD), and hepatocellular carcinoma (HCC) patients. Fecal specimens of nine healthy individuals, 11 CLD, and 21 HCC were collected. The diversity of gut microbiota was examined by PCR and Illumina MiSeq sequencing and analyzed using 16S rRNA gene sequencing database. The correlations between gut microbiota and the clinical parameters of participants were also addressed. Compared to healthy individuals, Firmicutes at a phylum level decreased in CLD and HCC patients and Proteobacteria increased (p < 0.05). The composition of Blautia on a genus level in CLD and HCC patients significantly decreased compared to healthy controls (p < 0.05). Firmicutes composition was negatively associated with age and number of males (p < 0.05) and was positively associated with monocytes, high-density lipoprotein cholesterol (HDL-C), and estimated glomerular filtration rate (eGFR) levels (p < 0.05). At a genus level, Blautia composition was negatively associated with cirrhosis, age, and number of males (p < 0.01), while it was positively associated with red blood cells (RBCs), triglycerides, HDL-C, and lymphocyte levels (p < 0.05). Conclusively, there was a significant compositional difference in gut microbiota in CLD and HCC patients compared with healthy subjects. Firmicutes and Blautia in gut microbiota system lessened in CLD and HCC patients. Clinical biochemical parameters have an impact on the diversity of gut microbiota in liver diseases.
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Affiliation(s)
- Tianyou Chen
- Department of Interventional Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Rongrong Ding
- Department of Hepatobiliary Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaorong Chen
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yunfei Lu
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jia Shi
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Ying Lü
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bozong Tang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wensi Zhang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chen Ye
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Yuan
- Department of Interventional Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Min Yuan Department of Interventional Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai200083, China
| | - Zongguo Yang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- CONTACT Zongguo Yang Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai201508, China
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Feng C, Liu W, Chen H, Dong W, Yang J. Effect of dark environment on intestinal flora and expression of genes related to liver metabolism in zebrafish (Danio rerio). Comp Biochem Physiol C Toxicol Pharmacol 2021; 249:109100. [PMID: 34174412 DOI: 10.1016/j.cbpc.2021.109100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
To explore the effects of dark environment on intestinal flora and expression of genes related to liver metabolism in zebrafish, a total of 60 zebrafish were fed for 21 days (24 h dark treatments or 14/10 h light/dark cycle), and the influence of dark environment on gut microbes and liver gene expression was studied using sequencing analysis of intestinal flora and liver. The results showed that the body weight of fish was significantly increased in the dark group than that in the control group (P < 0.05). Compared with the control group, dark environment treatment changed the composition of dominant flora, increased the abundance of unconventional bacteria and reduced probiotics in the intestine of zebrafish. Of these, the ratio of Bacteroidetes to Firmicutes in the intestine was reduced. The genome expression of the liver showed significant changes, and liver metabolites were also affected. Meanwhile, dark environment decreased gene expression associated with changes in blood glucose, lipid metabolism and immunization. Dark environment also caused liver steatosis as observed by histological study. This study shows that dark environment treatment has an important impact on liver metabolism and intestinal microbes in zebrafish.
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Affiliation(s)
- Chi Feng
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028000, China
| | - Wuyun Liu
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028000, China; School of Animal Science, Mongolian State University of Agriculture, Bayangol, Ulaanbaatar, Mongolia
| | - Hao Chen
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028000, China
| | - Wu Dong
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028000, China
| | - Jingfeng Yang
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028000, China.
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Chmielowska C, Korsak D, Chapkauskaitse E, Decewicz P, Lasek R, Szuplewska M, Bartosik D. Plasmidome of Listeria spp.-The repA-Family Business. Int J Mol Sci 2021; 22:ijms221910320. [PMID: 34638661 PMCID: PMC8508797 DOI: 10.3390/ijms221910320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth insight into the structure, diversity and evolution of plasmids occurring in Listeria strains inhabiting various environments under different anthropogenic pressures. Apart from the components of the conserved plasmid backbone (providing replication, stable maintenance and conjugational transfer functions), these replicons contain numerous adaptive genes possibly involved in: (i) resistance to antibiotics, heavy metals, metalloids and sanitizers, and (ii) responses to heat, oxidative, acid and high salinity stressors. Their genomes are also enriched by numerous transposable elements, which have influenced the plasmid architecture. The plasmidome of Listeria is dominated by a group of related replicons encoding the RepA replication initiation protein. Detailed comparative analyses provide valuable data on the level of conservation of these replicons and their role in shaping the structure of the Listeria pangenome, as well as their relationship to plasmids of other genera of Firmicutes, which demonstrates the range and direction of flow of genetic information in this important group of bacteria.
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Affiliation(s)
- Cora Chmielowska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (E.C.); (R.L.); (M.S.)
- Correspondence: (C.C.); (D.B.)
| | - Dorota Korsak
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
| | - Elvira Chapkauskaitse
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (E.C.); (R.L.); (M.S.)
| | - Przemysław Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
| | - Robert Lasek
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (E.C.); (R.L.); (M.S.)
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (E.C.); (R.L.); (M.S.)
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (E.C.); (R.L.); (M.S.)
- Correspondence: (C.C.); (D.B.)
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Stražar M, Mourits VP, Koeken VACM, de Bree LCJ, Moorlag SJCFM, Joosten LAB, van Crevel R, Vlamakis H, Netea MG, Xavier RJ. The influence of the gut microbiome on BCG-induced trained immunity. Genome Biol 2021; 22:275. [PMID: 34551799 PMCID: PMC8456614 DOI: 10.1186/s13059-021-02482-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/30/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. RESULTS Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling after 2 weeks and 3 months. Metagenomics based on de novo genome assembly reveals 43 immunomodulatory taxa. The nonspecific, trained immune response is detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlates with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, is associated positively with Ruminococcus and Eggerthella lenta. The identified immunomodulatory taxa also have the strongest effects on circulating metabolites, with Roseburia affecting phenylalanine metabolism. This is corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. CONCLUSIONS Variability in cytokine production after BCG vaccination is associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia is found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.
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Affiliation(s)
| | - Vera P Mourits
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Simone J C F M Moorlag
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Abstract
The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.
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Affiliation(s)
- Sandesh Acharya
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Amol Dahal
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
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Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJR, Forster SC, Cormie C, Goulding D, Lawley TD. Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle. Genome Biol 2021; 22:204. [PMID: 34348764 PMCID: PMC8340488 DOI: 10.1186/s13059-021-02428-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biological adaptations underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown. RESULTS We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria. CONCLUSIONS Our results suggest host adaptation in gut Firmicutes is an evolutionary trade-off between transmission range and colonization abundance. We reveal host transmission as an underappreciated process that shapes the evolution, assembly, and functions of gut Firmicutes.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| | - Alexandre Almeida
- Wellcome Sanger Institute, Hinxton, UK
- European Bioinformatics Institute, Hinxton, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Kevin Vervier
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | | | - Elisa Viciani
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas J R Dawson
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | | | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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Bindari YR, Moore RJ, Van TTH, Hilliar M, Wu SB, Walkden-Brown SW, Gerber PF. Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum. PLoS One 2021; 16:e0255633. [PMID: 34351989 PMCID: PMC8341621 DOI: 10.1371/journal.pone.0255633] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.
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Affiliation(s)
- Yugal R. Bindari
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Robert J. Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Matthew Hilliar
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Shu-Biao Wu
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W. Walkden-Brown
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Priscilla F. Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
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Mo J, Gao L, Zhang N, Xie J, Li D, Shan T, Fan L. Structural and quantitative alterations of gut microbiota in experimental small bowel obstruction. PLoS One 2021; 16:e0255651. [PMID: 34347831 PMCID: PMC8336877 DOI: 10.1371/journal.pone.0255651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 07/21/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE To investigate structural and quantitative alterations of gut microbiota in an experimental model of small bowel obstruction. METHOD A rat model of small bowel obstruction was established by using a polyvinyl chloride ring surgically placed surrounding the terminal ileum. The alterations of gut microbiota were studied after intestinal obstruction. Intraluminal fecal samples proximal to the obstruction were collected at different time points (24, 48 and 72 hours after obstruction) and analyzed by 16s rDNA high-throughput sequencing technology and quantitative PCR (qPCR) for target bacterial groups. Furthermore, intestinal claudin-1 mRNA expression was examined by real-time polymerase chain reaction analysis, and serum sIgA, IFABP and TFF3 levels were determined by enzyme-linked immunosorbent assay. RESULTS Small bowel obstruction led to significant bacterial overgrowth and profound alterations in gut microbiota composition and diversity. At the phylum level, the 16S rDNA sequences showed a marked decrease in the relative abundance of Firmicutes and increased abundance of Proteobacteria, Verrucomicrobia and Bacteroidetes. The qPCR analysis showed the absolute quantity of total bacteria increased significantly within 24 hours but did not change distinctly from 24 to 72 hours. Further indicators of intestinal mucosa damage and were observed as claudin-1 gene expression, sIgA and TFF3 levels decreased and IFABP level increased with prolonged obstruction. CONCLUSION Small bowel obstruction can cause significant structural and quantitative alterations of gut microbiota and induce disruption of gut mucosa barrier.
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MESH Headings
- Animals
- Bacteroidetes/genetics
- Claudin-1/genetics
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Disease Models, Animal
- Feces/microbiology
- Firmicutes/genetics
- Gastrointestinal Microbiome/genetics
- Gene Expression
- Ileum/microbiology
- Ileum/pathology
- Immunoglobulin A, Secretory/blood
- Immunoglobulin A, Secretory/metabolism
- Intestinal Mucosa/immunology
- Intestinal Mucosa/metabolism
- Intestinal Mucosa/microbiology
- Intestinal Obstruction/blood
- Intestinal Obstruction/microbiology
- Male
- Phylogeny
- Proteobacteria/genetics
- RNA, Ribosomal, 16S/genetics
- Rats
- Rats, Wistar
- Verrucomicrobia/genetics
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Affiliation(s)
- Jiali Mo
- Graduate school of Tianjin Medical University, Tianjin, China
| | - Lei Gao
- Graduate school of Tianjin Medical University, Tianjin, China
| | - Nan Zhang
- Department of Gastrointestinal Surgery, Nankai Hospital, Tianjin, China
| | - Jiliang Xie
- Department of Gastrointestinal Surgery, Nankai Hospital, Tianjin, China
| | - Donghua Li
- Department of Pharmacology, Tianjin Nankai Hospital, Tianjin, China
| | - Tao Shan
- Department of Gastrointestinal Surgery, Nankai Hospital, Tianjin, China
| | - Liuyang Fan
- Graduate school of Tianjin Medical University, Tianjin, China
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Toro‐Valdivieso C, Toro F, Stubbs S, Castro‐Nallar E, Blacklaws B. Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii). Microbiologyopen 2021; 10:e1215. [PMID: 34459554 PMCID: PMC8302013 DOI: 10.1002/mbo3.1215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host-microbial-environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 region of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla: Firmicutes (40% ±24), Fusobacteria (30% ±17), Bacteroidetes (22% ±10), Proteobacteria (6% ±4), and Actinobacteria (2% ±3). Alpha diversity was higher in Tierras Blancas. However, location was not found to be a dominant driver of microbial composition. Interestingly, the strongest signal in the data was a negative association between the genera Peptoclostridium and Fusobacterium, which explained 29.7% of the total microbial composition variability between samples. The genus Peptoclostridium has not been reported in other pinniped studies, and its role here is unclear, with interpretation challenging due to a lack of information regarding microbiome functionality in marine mammals. As a first insight into the JFFS fecal microbiome, these results contribute towards our understanding of the natural microbial diversity and composition in free-ranging pinnipeds.
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Affiliation(s)
| | - Frederick Toro
- Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
- Escuela de Medicina VeterinariaFacultad de Recursos Naturales y Medicina VeterinariaUniversidad Santo TomásViña del MarChile
- ONG PanthalassaRed de Estudios de Vertebrados Marinos en ChileSantiagoChile
- Ph.D. Program in Conservation MedicineFacultad de Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | - Samuel Stubbs
- Department of Infectious Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eduardo Castro‐Nallar
- Center for Bioinformatics and Integrative BiologyUniversidad Andres BelloSantiagoChile
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Kim PS, Shin NR, Lee JB, Kim MS, Whon TW, Hyun DW, Yun JH, Jung MJ, Kim JY, Bae JW. Host habitat is the major determinant of the gut microbiome of fish. Microbiome 2021; 9:166. [PMID: 34332628 PMCID: PMC8325807 DOI: 10.1186/s40168-021-01113-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. RESULTS We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). CONCLUSIONS Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
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Affiliation(s)
- Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Jae-Bong Lee
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Gijang-eup, Busan, 46083 Republic of Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Joon Yong Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
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Collins KH, Schwartz DJ, Lenz KL, Harris CA, Guilak F. Taxonomic changes in the gut microbiota are associated with cartilage damage independent of adiposity, high fat diet, and joint injury. Sci Rep 2021; 11:14560. [PMID: 34267289 PMCID: PMC8282619 DOI: 10.1038/s41598-021-94125-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/30/2021] [Indexed: 12/02/2022] Open
Abstract
Lipodystrophic mice are protected from cartilage damage following joint injury. This protection can be reversed by the implantation of a small adipose tissue graft. The purpose of this study was to evaluate the relationship between the gut microbiota and knee cartilage damage while controlling for adiposity, high fat diet, and joint injury using lipodystrophic (LD) mice. LD and littermate control (WT) mice were fed a high fat diet, chow diet, or were rescued with fat implantation, then challenged with destabilization of the medial meniscus surgery to induce osteoarthritis (OA). 16S rRNA sequencing was conducted on feces. MaAslin2 was used to determine associations between taxonomic relative abundance and OA severity. While serum LPS levels between groups were similar, synovial fluid LPS levels were increased in both limbs of HFD WT mice compared to all groups, except for fat transplanted animals. The Bacteroidetes:Firmicutes ratio of the gut microbiota was significantly reduced in HFD and OA-rescued animals when compared to chow. Nine novel significant associations were found between gut microbiota taxa and OA severity. These findings suggest the presence of causal relationships the gut microbiome and cartilage health, independent of diet or adiposity, providing potential therapeutic targets through manipulation of the microbiome.
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Affiliation(s)
- Kelsey H Collins
- Department of Orthopaedic Surgery, Washington University, Couch Building Room 3213, 4523 Clayton Avenue, St Louis, MO, 63110, USA
- Shriners Hospitals for Children, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University, St. Louis, MO, USA
| | - Drew J Schwartz
- Division of Infectious Diseases, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristin L Lenz
- Department of Orthopaedic Surgery, Washington University, Couch Building Room 3213, 4523 Clayton Avenue, St Louis, MO, 63110, USA
- Shriners Hospitals for Children, St. Louis, MO, USA
| | - Charles A Harris
- Division of Endocrinology, Washington University, St. Louis, MO, USA
- Early Clinical Development & Experimental Sciences, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University, Couch Building Room 3213, 4523 Clayton Avenue, St Louis, MO, 63110, USA.
- Shriners Hospitals for Children, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University, St. Louis, MO, USA.
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65
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Fu H, Zhang L, Fan C, Liu C, Li W, Cheng Q, Zhao X, Jia S, Zhang Y. Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals. Microb Biotechnol 2021; 14:1300-1315. [PMID: 33369229 PMCID: PMC8313255 DOI: 10.1111/1751-7915.13687] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/07/2020] [Indexed: 02/01/2023] Open
Abstract
The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.
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Affiliation(s)
- Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Shangang Jia
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
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Abstract
A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
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Affiliation(s)
- Ruochen Jiang
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
| | - Wei Vivian Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, 08854, NJ, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, 90095-7088, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, 90095-1766, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, 90095-1772, CA, USA.
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Low A, Soh M, Miyake S, Aw VZJ, Feng J, Wong A, Seedorf H. Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract. Int J Mol Sci 2021; 22:5981. [PMID: 34205981 PMCID: PMC8198505 DOI: 10.3390/ijms22115981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 01/04/2023] Open
Abstract
Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance of expanding sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.
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Affiliation(s)
- Adrian Low
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Sou Miyake
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Vanessa Zhi Jie Aw
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Jian Feng
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Adeline Wong
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore; (A.L.); (M.S.); (S.M.); (V.Z.J.A.); (J.F.); (A.W.)
- Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
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Moreira Júnior RE, de Carvalho LM, Dos Reis DC, Cassali GD, Faria AMC, Maioli TU, Brunialti-Godard AL. Diet-induced obesity leads to alterations in behavior and gut microbiota composition in mice. J Nutr Biochem 2021; 92:108622. [PMID: 33705942 DOI: 10.1016/j.jnutbio.2021.108622] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/30/2020] [Accepted: 02/04/2021] [Indexed: 12/17/2022]
Abstract
The high prevalence of obesity and associated metabolic disorders are one of the major public health problems worldwide. Among the main causal factors of obesity, excessive consumption of food rich in sugar and fat stands out due to its high energy density. The regulation of food intake relies on hypothalamic control by the action of several neuropeptides. Excessive consumption of hypercaloric diets has impact in the behavior and in the gut microbiota. In the present study, we used a high-sugar and fat (HSB) diet for 12 weeks to induce obesity in C57BL/6 mice and to investigate its effects on the gut microbiota, hypothalamic peptides, and behavior. We hypothesize that chronic consumption of HSB diet can change the behavior. Additionally, we also hypothesize that changes in gut microbiota can be associated with changes in the transcriptional regulation of hypothalamic peptides and behavior. To evaluate the gut microbiota, we performed the sequencing of 16S rRNA gene, which demonstrate that HSB diet modulates the gut microbiota with an increase in the Firmicutes and Actinobacteria phylum and a decrease of Bacteroidetes phylum. The real time qPCR revealed that HSB-fed mice presented changes in the transcriptional regulation of hypothalamic neuropeptides genes such as Npy, Gal and Galr1. The Marble-burying and Light/dark box tests also showed an alteration in anxiety and impulsive behaviors for the HSB-fed mice. Our data provides evidence that obesity induced by HSB diet consumption is associated with alterations in gut microbiota and behavior, highlighting the multifactorial characteristics of this disease.
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Affiliation(s)
- Renato Elias Moreira Júnior
- Laboratório de Genética Animal e Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luana Martins de Carvalho
- Laboratório de Genética Animal e Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Diego Carlos Dos Reis
- Laboratório de Patologia Comparada, Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Geovanni Dantas Cassali
- Laboratório de Patologia Comparada, Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Maria Caetano Faria
- Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Tatiani Uceli Maioli
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Lúcia Brunialti-Godard
- Laboratório de Genética Animal e Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Jiang W, Yu X, Kosik RO, Song Y, Qiao T, Tong J, Liu S, Fan S, Luo Q, Chai L, Lv Z, Li D. Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease. Thyroid 2021; 31:810-820. [PMID: 33234057 PMCID: PMC8110022 DOI: 10.1089/thy.2020.0193] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Gut microbiota are considered to be intrinsic regulators of thyroid autoimmunity. We designed a cross-sectional study to examine the makeup and metabolic function of microbiota in Graves' disease (GD) patients, with the ultimate aim of offering new perspectives on the diagnosis and treatment of GD. Methods: The 16S ribosomal RNA (rRNA) V3-V4 DNA regions of microbiota were obtained from fecal samples collected from 45 GD patients and 59 controls. Microbial differences between the two groups were subsequently analyzed based on high-throughput sequencing. Results: Compared with controls, GD patients had reduced alpha diversity (p < 0.05). At the phylum level, GD patients had a significantly lower proportion of Firmicutes (p = 0.008) and a significantly higher proportion of Bacteroidetes (p = 0.002) compared with the controls. At the genus level, GD patients had greater numbers of Bacteroides and Lactobacillus, although fewer Blautia, [Eubacterium]_hallii_group, Anaerostipes, Collinsella, Dorea, unclassified_f_Peptostreptococcaceae, and [Ruminococcus]_torques_group than controls (all p < 0.05). Subgroup analysis of GD patients revealed that Lactobacillus may play a key role in the pathogenesis of autoimmune thyroid diseases. Nine distinct genera showed significant correlations with certain thyroid function tests. Functional prediction revealed that Blautia may be an important microbe in certain metabolic pathways that occur in the hyperthyroid state. In addition, linear discriminant analysis (LDA) and effect size (LEfSe) analysis showed that there were significant differences in the levels of 18 genera between GD patients and controls (LDA >3.0, all p < 0.05). A diagnostic model using the top nine genera had an area under the curve of 0.8109 [confidence interval: 0.7274-0.8945]. Conclusions: Intestinal microbiota are different in GD patients. The microbiota we identified offer an alternative noninvasive diagnostic methodology for GD. Microbiota may also play a role in thyroid autoimmunity, and future research is needed to further elucidate the role.
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Affiliation(s)
- Wen Jiang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaqing Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Russell Oliver Kosik
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yingchun Song
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tingting Qiao
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junyu Tong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Simin Liu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Suyun Fan
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiong Luo
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Address correspondence to: Zhongwei Lv, PhD, MD, Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Dan Li
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Address correspondence to: Dan Li, PhD, MD, Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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Li X, Hui Y, Leng B, Ren J, Song Y, Che L, Peng X, Huang B, Liu S, Li L, Nielsen DS, Li Y, Dai X, Zhao S. Millet-based supplement restored gut microbial diversity of acute malnourished pigs. PLoS One 2021; 16:e0250423. [PMID: 33914799 PMCID: PMC8084169 DOI: 10.1371/journal.pone.0250423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
The tight association between malnutrition and gut microbiota (GM) dysbiosis enables microbiota-targeting intervention to be a promising strategy. Thus, we used a malnourished pig model to investigate the host response and GM alterations under different diet supplementation strategies. Pigs at age of 4 weeks were fed with pure maize diet to induce malnutrition symptoms, and followed by continuous feeding with maize (Maize, n = 8) or re-feeding using either corn-soy-blend (CSB+, n = 10) or millet-soy-blend based (MSB+, n = 10) supplementary food for 3 weeks. Meanwhile, 8 pigs were fed on a standard formulated ration as control (Ref). The effect of nutritional supplementation was assessed by the growth status, blood chemistry, gastrointestinal pathology, mucosal microbiota composition and colon production of short-chain fatty acids. Compared with purely maize-fed pigs, both CSB+ and MSB+ elevated the concentrations of total protein and globulin in blood. These pigs still showed most malnutrition symptoms after the food intervention period. MSB+ had superior influence on the GM development, exhibiting better performance in both structural and functional aspects. MSB+ pigs were colonized by less Proteobacteria but more Bacteroidetes, Firmicutes and Lachnospira spp. Pearson's correlation analysis indicated a strong correlation between the abundance of mucosal e.g., Faecalibacterium and Lachnospira spp. and body weight, crown-rump length and total serum protein. In conclusion, the malnutrition symptoms were accompanied by an aberrant GM, and millet-based nutritional supplementation showed promising potentials to restore the reduced GM diversity implicated in pig malnutrition.
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Affiliation(s)
- Xuejing Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Yan Hui
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bingfeng Leng
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
- Neomics Institute, Life and Science Park 301, Pingshan, Shenzhen, China
| | - Junli Ren
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Yanni Song
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Lianqiang Che
- Animal Nutrition Institute, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Xi Peng
- College of Life Science, China West Normal University, Nanchong, China
| | - Baojia Huang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Songling Liu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Lin Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, China
| | | | - Yong Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, China
| | - Xiaoshuang Dai
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
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Zheng X, Zhu Q, Zhou Z, Wu F, Chen L, Cao Q, Shi F. Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits. PLoS One 2021; 16:e0250675. [PMID: 33901256 PMCID: PMC8075264 DOI: 10.1371/journal.pone.0250675] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/12/2021] [Indexed: 01/04/2023] Open
Abstract
Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.
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Affiliation(s)
- Xiang Zheng
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology, Baoding, China
| | - Qidi Zhu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Zhijun Zhou
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Fangtong Wu
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology, Baoding, China
| | - Lixuan Chen
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Qianrong Cao
- Laboratory of Enzyme Preparation, Hebei Research Institute of Microbiology, Baoding, China
| | - Fuming Shi
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
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Krupka M, Raskova Kafkova L, Barkocziova L, Sloupenska K, Brokesova D, Sebela M, Raska M. Preparation and properties of recombinant Clostridium ramosum IgA proteinase. Isolation of Fc-SC and Fab fragments of human secretory IgA. Protein Expr Purif 2021; 184:105891. [PMID: 33895263 DOI: 10.1016/j.pep.2021.105891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/23/2021] [Accepted: 04/17/2021] [Indexed: 11/17/2022]
Abstract
Immunoglobulin A (IgA) proteinase from Clostridium ramosum is the enzyme which cleaves IgA of both subclasses; in contrast, the other bacterial proteinases cleave only IgA1 proteins. Previous reports characterized the activity of proteinase naturally secreted by C. ramosum specific for the normal human serum IgA of IgA1 and IgA2m(1) subclasses and also for secretory IgA (SIgA). Its amino acid sequence was determined, and the recombinant proteinase which cleaved IgA of both subclasses was prepared. Here we report the optimized expression, purification, storage conditions and activity testing against purified human milk SIgA. The recombinant C. ramosum IgA proteinase isolated in the high degree of purity exhibited almost complete cleavage of SIgA of both subclasses. The proteinase remained active upon storage for more than 10 month at -20 °C without substantial loss of enzymatic activity. Purified SIgA fragments are suitable for studies of all antigen-binding and Fc-dependent functions of SIgA involved in the protection against infections with mucosal pathogens.
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Affiliation(s)
- Michal Krupka
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Leona Raskova Kafkova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.
| | - Lucia Barkocziova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Kristyna Sloupenska
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Diana Brokesova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Marek Sebela
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Olomouc, Czech Republic
| | - Milan Raska
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.
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Gal A, Barko PC, Biggs PJ, Gedye KR, Midwinter AC, Williams DA, Burchell RK, Pazzi P. One dog's waste is another dog's wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome. PLoS One 2021; 16:e0250344. [PMID: 33872339 PMCID: PMC8055013 DOI: 10.1371/journal.pone.0250344] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/05/2021] [Indexed: 01/04/2023] Open
Abstract
Canine acute hemorrhagic diarrhea syndrome (AHDS) has been associated in some studies with Clostridioides perfringens overgrowth and toxin-mediated necrosis of the intestinal mucosa. We aimed to determine the effect of a single fecal microbiota transplantation (FMT) on clinical scores and fecal microbiomes of 1 and 7 dogs with AHDS from New Zealand and South Africa. We hypothesized that FMT would improve AHDS clinical scores and increase microbiota alpha-diversity and short-chain fatty acid (SCFA)-producing microbial communities’ abundances in dogs with AHDS after FMT. We sequenced the V3-V4 region of the 16S-rRNA gene in the feces of AHDS FMT-recipients and sham-treated control dogs, and their healthy donors at admission, discharge, and 30 days post-discharge. There were no significant differences in median AHDS clinical scores between FMT-recipients and sham-treated controls at admission or discharge (P = 0.22, P = 0.41). At admission, the Shannon diversity index (SDI) was lower in AHDS dogs than healthy donors (P = 0.002). The SDI did not change from admission to 30 days in sham-treated dogs yet increased in FMT-recipients from admission to discharge (P = 0.04) to levels not different than donors (P = 0.33) but significantly higher than sham-treated controls (P = 0.002). At 30 days, the SDI did not differ between FMT recipients, sham-treated controls, and donors (P = 0.88). Principal coordinate analysis of the Bray-Curtis index separated post-FMT and donor dogs from pre-FMT and sham-treated dogs (P = 0.009) because of increased SCFA-producing genera’s abundances after FMT. A single co-abundance subnetwork contained many of the same OTUs found to be differentially abundant in FMT-recipients, and the abundance of this module was increased in FMT-recipients at discharge and 30 days, compared to sham-treated controls. We conclude in this small pilot study FMT did not have any clinical benefit. A single FMT procedure has the potential to increase bacterial communities of SCFA-producing genera important for intestinal health up to 30 days post-FMT.
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Affiliation(s)
- Arnon Gal
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Patrick C. Barko
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Patrick J. Biggs
- Molecular Epidemiology & Public Health Laboratory, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Bioinformatics and Statistics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Kristene R. Gedye
- Molecular Epidemiology & Public Health Laboratory, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- Molecular Epidemiology & Public Health Laboratory, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A. Williams
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Richard K. Burchell
- North Coast Veterinary and Referral Centre, Sunshine Coast, Queensland, Australia
| | - Paolo Pazzi
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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Abstract
BACKGROUND Common bile duct (CBD) stone is one of the most prevalent gastroenterological diseases, but the role played by biliary microbiota in the pathogenesis of CBD stones remains obscure. The aim of this study was to investigate the characteristics of the biliary tract core microbiome and its potential association with the formation of pigment stones. METHODS Twenty-eight patients with biliary obstruction of various causes were enrolled. Thirteen had new-onset pigment CBD stone. Of the remaining 15, four had benign biliary stricture, four had gallbladder cancer, three had pancreatic cancer, 3 had distal CBD cancer, and one had hepatocellular carcinoma. Endoscopic retrograde cholangiopancreatography was used to collect bile samples for DNA extraction, 16S ribosomal RNA gene sequencing, and bile microbiota composition analysis. RESULTS Proteobacteria (61.7%), Firmicutes (25.1%), Bacteroidetes (5%), Fusobacteria (4.6%), and Actinobacteria (2.6%) were the most dominant phyla in the bile of the 28 study subjects. A comparison between new-onset choledocholithiasis and other causes of biliary obstruction (controls) showed Enterococcus was found to be significantly abundant in the CBD stone group at the genus level (linear discriminant analysis score = 4.38; P = 0.03). However, no other significant compositional difference was observed. CONCLUSION This study demonstrates an abundance of microbiota in bile juice and presents a biliary microbiome composition similar to that of duodenum. The study also shows Enterococcus was significantly abundant in the bile juice of patients with a brown pigment stone than in controls, which suggests Enterococcus may play an important role in the development of pigment stones.
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Affiliation(s)
- Boram Kim
- Digestive Disease Center, Department of Internal Medicine, Inha University School of Medicine, Incheon, Korea
| | - Jin Seok Park
- Digestive Disease Center, Department of Internal Medicine, Inha University School of Medicine, Incheon, Korea.
| | - Jaewoong Bae
- Hecto Innovation Lab., Hecto Co., Ltd., Seoul, Korea
| | - Nakwon Hwang
- Hecto Innovation Lab., Hecto Co., Ltd., Seoul, Korea
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Park SA, Lee GH, Hoang TH, Lee HY, Kang IY, Chung MJ, Jin JS, Chae HJ. Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats. PLoS One 2021; 16:e0250354. [PMID: 33872333 PMCID: PMC8055018 DOI: 10.1371/journal.pone.0250354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/05/2021] [Indexed: 01/08/2023] Open
Abstract
Constipation is a common condition that affects individuals of all ages, and prolonged constipation needs to be prevented to avoid potential complications and reduce the additional stress on individuals with pre-medical conditions. This study aimed to evaluate the effects of heat-inactivated Lactobacillus plantarum (HLp-nF1) on loperamide-induced constipation in rats. Constipation-induced male rats were treated orally with low to high doses of HLp-nF1 and an anti-constipation medication Dulcolax for five weeks. Study has 8 groups, control group; loperamide-treated group; Dulcolax-treated group; treatment with 3.2 × 1010, 8 × 1010 and 1.6 × 1011, cells/mL HLp-nF1; Loperamide + Dulcolax treated group. HLp-nF1 treated rats showed improvements in fecal pellet number, weight, water content, intestinal transit length, and contractility compared to the constipation-induced rats. Also, an increase in the intestine mucosal layer thickness and the number of mucin-producing crypt epithelial cells were observed in HLp-nF1-treated groups. Further, the levels of inflammatory cytokines levels were significantly downregulated by treatment with HLp-nF1 and Dulcolax. Notably, the metagenomics sequencing analysis demonstrated a similar genus pattern to the pre-preparation group and control with HLp-nF1 treatment. In conclusion, the administration of >3.2 × 1010 cells/mL HLp-nF1 has a positive impact on the constipated rats overall health.
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Affiliation(s)
- Seon-Ah Park
- Non-Clinical Evaluation Center, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
| | - Geum-Hwa Lee
- Non-Clinical Evaluation Center, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
| | - The-Hiep Hoang
- Non-Clinical Evaluation Center, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
- Department of Pharmacology and Institute of New Drug Development, School of Medicine, Jeonbuk National University, Jeonju, South Korea
| | - Hwa-Young Lee
- Non-Clinical Evaluation Center, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
- Department of Pharmacology and Institute of New Drug Development, School of Medicine, Jeonbuk National University, Jeonju, South Korea
| | | | - Myong-Ja Chung
- Department of Pathology, Jeonbuk National University Medical School, Jeonju, Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, Iksan, South Korea
| | - Han-Jung Chae
- Non-Clinical Evaluation Center, Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
- Department of Pharmacology and Institute of New Drug Development, School of Medicine, Jeonbuk National University, Jeonju, South Korea
- * E-mail:
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Goossens E, Boonyarittichaikij R, Dekeukeleire D, Van Praet S, Bonte D, Verheyen K, Lens L, Martel A, Verbrugghe E. Exploring the faecal microbiome of the Eurasian nuthatch (Sitta europaea). Arch Microbiol 2021; 203:2119-2127. [PMID: 33606040 DOI: 10.1007/s00203-021-02195-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/08/2020] [Accepted: 02/04/2021] [Indexed: 01/12/2023]
Abstract
Gastrointestinal microbiota fulfill pivotal roles in providing a host with nutrition and protection from pathogenic microorganisms. Up to date, most microbiota research has focused on humans and other mammals, whereas birds and especially wild birds lag behind. Within the field of the avian gut microbiome, research is heavily biased towards poultry. In this study, we analyzed the gut microbiome of the Eurasian nuthatch (Sitta europaea), using faecal samples of eight nestlings originating from three nuthatch nests in the south of Ghent (Belgium), using Illumina sequencing of the 16S rRNA gene. Relative frequency analysis showed a dominance of Firmicutes and Actinobacteria and to a lesser extent Proteobacteria. Bacteroidetes and other phyla were relatively rare. At higher taxonomic levels, a high degree of inter-individual variation in terms of overall microbiota community structure as well as dominance of certain bacteria was observed, but with a higher similarity for the nestlings sharing the same nest. When comparing the nuthatch faecal microbiome to that of great tit nestlings that were sampled during the same breeding season and in the same forest fragment, differences in the microbial community structure were observed, revealing distinct dissimilarities in the relative abundancy of taxa between the two bird species. This study is the first report on the nuthatch microbiome and serves as a reference study for nuthatch bacterial diversity and can be used for targeted screening of the composition and general functions of the avian gut microbiome.
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Affiliation(s)
- Evy Goossens
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Roschong Boonyarittichaikij
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Phuttamonthon, Nakhon Pathom, 73170, Thailand
| | - Daan Dekeukeleire
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Sarah Van Praet
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Kris Verheyen
- Forest and Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090, Gontrode, Belgium
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Elin Verbrugghe
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
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Abstract
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
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MESH Headings
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/metabolism
- Base Pairing
- Base Sequence
- Clostridiales/classification
- Clostridiales/genetics
- Clostridiales/metabolism
- Firmicutes/classification
- Firmicutes/genetics
- Firmicutes/metabolism
- Genome, Archaeal
- Genome, Bacterial
- Halobacteriales/classification
- Halobacteriales/genetics
- Halobacteriales/metabolism
- Nucleic Acid Conformation
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Thermoanaerobacterium/classification
- Thermoanaerobacterium/genetics
- Thermoanaerobacterium/metabolism
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Affiliation(s)
- Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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Noh H, Jang HH, Kim G, Zouiouich S, Cho SY, Kim HJ, Kim J, Choe JS, Gunter MJ, Ferrari P, Scalbert A, Freisling H. Taxonomic Composition and Diversity of the Gut Microbiota in Relation to Habitual Dietary Intake in Korean Adults. Nutrients 2021; 13:366. [PMID: 33530330 PMCID: PMC7912254 DOI: 10.3390/nu13020366] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/14/2023] Open
Abstract
We investigated associations of habitual dietary intake with the taxonomic composition and diversity of the human gut microbiota in 222 Koreans aged 18-58 years in a cross-sectional study. Gut microbiota data were obtained by 16S rRNA gene sequencing on DNA extracted from fecal samples. The habitual diet for the previous year was assessed by a food frequency questionnaire. After multivariable adjustment, intake of several food groups including vegetables, fermented legumes, legumes, dairy products, processed meat, and non-alcoholic beverages were associated with major phyla of the gut microbiota. A dietary pattern related to higher α-diversity (HiαDP) derived by reduced rank regression was characterized by higher intakes of fermented legumes, vegetables, seaweeds, and nuts/seeds and lower intakes of non-alcoholic beverages. The HiαDP was positively associated with several genera of Firmicutes such as Lactobacillus, Ruminococcus, and Eubacterium (all p < 0.05). Among enterotypes identified by principal coordinate analysis based on the β-diversity, the Ruminococcus enterotype had higher HiαDP scores and was strongly positively associated with intakes of vegetables, seaweeds, and nuts/seeds, compared to the two other enterotypes. We conclude that a plant- and fermented food-based diet was positively associated with some genera of Firmicutes (e.g., Lactobacillus, Ruminococcus, and Eubacterium) reflecting better gut microbial health.
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Affiliation(s)
- Hwayoung Noh
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), 69008 Lyon, France; (H.N.); (S.Z.); (M.J.G.); (P.F.); (A.S.)
- Department of Cancer Prevention and Environment, INSERM UA8, Léon Bérard Cancer Center, 69003 Lyon, France
| | - Hwan-Hee Jang
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do 55365, Korea; (H.-H.J.); (G.K.); (S.-Y.C.); (H.-J.K.); (J.-S.C.)
| | - Gichang Kim
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do 55365, Korea; (H.-H.J.); (G.K.); (S.-Y.C.); (H.-J.K.); (J.-S.C.)
| | - Semi Zouiouich
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), 69008 Lyon, France; (H.N.); (S.Z.); (M.J.G.); (P.F.); (A.S.)
| | - Su-Yeon Cho
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do 55365, Korea; (H.-H.J.); (G.K.); (S.-Y.C.); (H.-J.K.); (J.-S.C.)
| | - Hyeon-Jeong Kim
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do 55365, Korea; (H.-H.J.); (G.K.); (S.-Y.C.); (H.-J.K.); (J.-S.C.)
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea;
| | - Jeong-Sook Choe
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do 55365, Korea; (H.-H.J.); (G.K.); (S.-Y.C.); (H.-J.K.); (J.-S.C.)
| | - Marc J. Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), 69008 Lyon, France; (H.N.); (S.Z.); (M.J.G.); (P.F.); (A.S.)
| | - Pietro Ferrari
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), 69008 Lyon, France; (H.N.); (S.Z.); (M.J.G.); (P.F.); (A.S.)
| | - Augustin Scalbert
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), 69008 Lyon, France; (H.N.); (S.Z.); (M.J.G.); (P.F.); (A.S.)
| | - Heinz Freisling
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), 69008 Lyon, France; (H.N.); (S.Z.); (M.J.G.); (P.F.); (A.S.)
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Jobira B, Frank DN, Silveira LJ, Pyle L, Kelsey MM, Garcia-Reyes Y, Robertson CE, Ir D, Nadeau KJ, Cree-Green M. Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome. PLoS One 2021; 16:e0245219. [PMID: 33465100 PMCID: PMC7815089 DOI: 10.1371/journal.pone.0245219] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
Objective Hepatic steatosis (HS) is common in adolescents with obesity and polycystic ovary syndrome (PCOS). Gut microbiota are altered in adults with obesity, HS, and PCOS, which may worsen metabolic outcomes, but similar data is lacking in youth. Methods Thirty-four adolescents with PCOS and obesity underwent stool and fasting blood collection, oral glucose tolerance testing, and MRI for hepatic fat fraction (HFF). Fecal bacteria were profiled by high-throughput 16S rRNA gene sequencing. Results 50% had HS (N = 17, age 16.2±1.5 years, BMI 38±7 kg/m2, HFF 9.8[6.5, 20.7]%) and 50% did not (N = 17, age 15.8±2.2 years, BMI 35±4 kg/m2, HFF 3.8[2.6, 4.4]%). The groups showed no difference in bacterial α-diversity (richness p = 0.202; evenness p = 0.087; and diversity p = 0.069) or global difference in microbiota (β-diversity). Those with HS had lower % relative abundance (%RA) of Bacteroidetes (p = 0.013), Bacteroidaceae (p = 0.009), Porphyromonadaceae (p = 0.011), and Ruminococcaceae (p = 0.008), and higher Firmicutes:Bacteroidetes (F:B) ratio (47.8% vs. 4.3%, p = 0.018) and Streptococcaceae (p = 0.034). Bacterial taxa including phyla F:B ratio, Bacteroidetes, and family Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae correlated with metabolic markers. Conclusions Obese adolescents with PCOS and HS have differences in composition of gut microbiota, which correlate with metabolic markers, suggesting a modifying role of gut microbiota in HS and PCOS.
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Affiliation(s)
- Beza Jobira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Daniel N. Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Lori J. Silveira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Laura Pyle
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Megan M. Kelsey
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Yesenia Garcia-Reyes
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kristen J. Nadeau
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Melanie Cree-Green
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- * E-mail:
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80
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Lukoseviciute L, Lebedeva J, Kuisiene N. Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave. Microb Ecol 2021; 81:110-121. [PMID: 32638044 DOI: 10.1007/s00248-020-01554-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.
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Affiliation(s)
- Laima Lukoseviciute
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jolanta Lebedeva
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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81
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Yu Z, Shi Z, Zheng Z, Han J, Yang W, Lu R, Lin W, Zheng Y, Nie D, Chen G. DEHP induce cholesterol imbalance via disturbing bile acid metabolism by altering the composition of gut microbiota in rats. Chemosphere 2021; 263:127959. [PMID: 32814133 DOI: 10.1016/j.chemosphere.2020.127959] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Di(2-ethylhexyl) phthalate (DEHP) is one of the most widespread environmental contaminants worldwide because of its massive production, extensive use in common products, and liability to leach from products. This study investigated the mechanisms of DEHP mediated alteration of lipid metabolism. Rats were treated with 0.5 mg kg-1 d-1 of DEHP for 23 weeks. Results showed that the treatment induced cholesterol imbalance. Further fecal transplantation experiments corroborated the involvement of gut microbiota in DEHP-induced cholesterol imbalance. In addition, 16S rRNA gene sequencing analysis of cecal contents showed that DEHP disrupted the gut microbiota diversity in rats and increased the ratio of Firmicutes to Bacteroidetes. Further cecal metabolomic analyses, bile salt hydrolase enzyme activity, and gene expression examination revealed that chronic DEHP exposure generated a bile acid profile in the gut that is a more potent activator of farnesoid X receptor (FXR). The activation of FXR in the gut induced the expression of fibroblast growth factor 15, which subsequently suppressed cytochrome P450 family 7 subfamily A member 1 in the liver and bile acid synthesis. These results suggest that DEHP might induce cholesterol imbalance by regulating bile acid metabolism via the remodeling of the gut microbiota.
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Affiliation(s)
- Zhen Yu
- Fujian Provincial Key Laboratory of Medical Analysis, Fujian Academy of Medical Sciences, Fuzhou, 350001, China
| | - Zhenhua Shi
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zeyu Zheng
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Junyong Han
- Fujian Provincial Key Laboratory of Medical Analysis, Fujian Academy of Medical Sciences, Fuzhou, 350001, China
| | - Wencong Yang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Rongmei Lu
- Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Wei Lin
- Fujian Provincial Hospital, Fuzhou, 350001, China
| | | | - Daoshun Nie
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Gang Chen
- Fujian Provincial Key Laboratory of Medical Analysis, Fujian Academy of Medical Sciences, Fuzhou, 350001, China; Fujian Provincial Hospital, Fuzhou, 350001, China.
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82
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van Muijlwijk GH, van Mierlo G, Jansen PW, Vermeulen M, Bleumink-Pluym NM, Palm NW, van Putten JP, de Zoete MR. Identification of Allobaculum mucolyticum as a novel human intestinal mucin degrader. Gut Microbes 2021; 13:1966278. [PMID: 34455931 PMCID: PMC8409761 DOI: 10.1080/19490976.2021.1966278] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 02/04/2023] Open
Abstract
The human gut microbiota plays a central role in intestinal health and disease. Yet, many of its bacterial constituents are functionally still largely unexplored. A crucial prerequisite for bacterial survival and proliferation is the creation and/or exploitation of an own niche. For many bacterial species that are linked to human disease, the inner mucus layer was found to be an important niche. Allobaculum mucolyticum is a newly identified, IBD-associated species that is thought be closely associated with the host epithelium. To explore how this bacterium is able to effectively colonize this niche, we screened its genome for factors that may contribute to mucosal colonization. Up to 60 genes encoding putative Carbohydrate Active Enzymes (CAZymes) were identified in the genome of A. mucolyticum. Mass spectrometry revealed 49 CAZymes of which 26 were significantly enriched in its secretome. Functional assays demonstrated the presence of CAZyme activity in A. mucolyticum conditioned medium, degradation of human mucin O-glycans, and utilization of liberated non-terminal monosaccharides for bacterial growth. The results support a model in which sialidases and fucosidases remove terminal O-glycan sugars enabling subsequent degradation and utilization of carbohydrates for A. mucolyticum growth. A. mucolyticum CAZyme secretion may thus facilitate bacterial colonization and degradation of the mucus layer and may pose an interesting target for future therapeutic intervention.
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Affiliation(s)
- Guus H. van Muijlwijk
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), LausanneCH-1015, Switzerland
| | - Pascal W.T.C. Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jos P.M. van Putten
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
| | - Marcel R. de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
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83
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Lee SM, Kong HG, Song GC, Ryu CM. Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. ISME J 2021; 15:330-347. [PMID: 33028974 PMCID: PMC7852523 DOI: 10.1038/s41396-020-00785-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.
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Affiliation(s)
- Sang-Moo Lee
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Hyun Gi Kong
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 54875, South Korea
| | - Geun Cheol Song
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea.
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84
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Hamood Altowayti WA, Almoalemi H, Shahir S, Othman N. Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation. Ecotoxicol Environ Saf 2020; 205:111267. [PMID: 32992213 DOI: 10.1016/j.ecoenv.2020.111267] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/16/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.
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Affiliation(s)
- Wahid Ali Hamood Altowayti
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia; Micro-pollutant Research Centre (MPRC), Department of Civil Engineering, Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Johor, Malaysia.
| | - Hafedh Almoalemi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.
| | - Shafinaz Shahir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.
| | - Norzila Othman
- Micro-pollutant Research Centre (MPRC), Department of Civil Engineering, Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Johor, Malaysia.
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Abstract
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
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Affiliation(s)
- Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Colton J Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Cano-Ortiz A, Laborda-Illanes A, Plaza-Andrades I, Membrillo del Pozo A, Villarrubia Cuadrado A, Rodríguez Calvo de Mora M, Leiva-Gea I, Sanchez-Alcoholado L, Queipo-Ortuño MI. Connection between the Gut Microbiome, Systemic Inflammation, Gut Permeability and FOXP3 Expression in Patients with Primary Sjögren's Syndrome. Int J Mol Sci 2020; 21:ijms21228733. [PMID: 33228011 PMCID: PMC7699261 DOI: 10.3390/ijms21228733] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
The aims of this study were to explore intestinal microbial composition and functionality in primary Sjögren’s syndrome (pSS) and to relate these findings to inflammation, permeability and the transcription factor Forkhead box protein P3 (FOXP3) gene expression in peripheral blood. The study included 19 pSS patients and 19 healthy controls matched for age, sex, and body mass index. Fecal bacterial DNA was extracted and analyzed by 16S rRNA sequencing using an Ion S5 platform followed by a bioinformatics analysis using Quantitative Insights into Microbial Ecology (QIIME II) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our data suggest that the gut microbiota of pSS patients differs at both the taxonomic and functional levels with respect to healthy controls. The gut microbiota profile of our pSS patients was characterized by a lower diversity and richness and with Bacteroidetes dominating at the phylum level. The pSS patients had less beneficial or commensal butyrate-producing bacteria and a higher proportion of opportunistic pathogens with proinflammatory activity, which may impair intestinal barrier function and therefore contribute to inflammatory processes associated with pSS by increasing the production of proinflammatory cytokines and decreasing the release of the anti-inflammatory cytokine IL-10 and the peripheral FOXP3 mRNA expression, implicated in the development and function of regulatory T cells (Treg) cells. Further studies are needed to better understand the real impact of dysbiosis on the course of pSS and to conceive preventive or therapeutic strategies to counteract microbiome-driven inflammation.
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Affiliation(s)
- Antonio Cano-Ortiz
- Servicio de Oftalmología, Hospital de la Arruzafa. Universidad de Córdoba, 14012 Córdoba, Spain; (A.C.-O.); (A.M.d.P.); (A.V.C.)
| | - Aurora Laborda-Illanes
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, 29010 Málaga, Spain; (A.L.-I.); (I.P.-A.)
- Facultad de Medicina, Universidad de Málaga, 29071 Málaga, Spain
| | - Isaac Plaza-Andrades
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, 29010 Málaga, Spain; (A.L.-I.); (I.P.-A.)
| | - Alberto Membrillo del Pozo
- Servicio de Oftalmología, Hospital de la Arruzafa. Universidad de Córdoba, 14012 Córdoba, Spain; (A.C.-O.); (A.M.d.P.); (A.V.C.)
| | - Alberto Villarrubia Cuadrado
- Servicio de Oftalmología, Hospital de la Arruzafa. Universidad de Córdoba, 14012 Córdoba, Spain; (A.C.-O.); (A.M.d.P.); (A.V.C.)
| | | | - Isabel Leiva-Gea
- Unidad de Endocrinología Pediátrica, Hospital Materno-Infantil, 29009 Málaga, Spain;
| | - Lidia Sanchez-Alcoholado
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, 29010 Málaga, Spain; (A.L.-I.); (I.P.-A.)
- Facultad de Medicina, Universidad de Málaga, 29071 Málaga, Spain
- Correspondence: (L.S.-A.); (M.I.Q.-O.)
| | - María Isabel Queipo-Ortuño
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, 29010 Málaga, Spain; (A.L.-I.); (I.P.-A.)
- Correspondence: (L.S.-A.); (M.I.Q.-O.)
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Patin NV, Peña-Gonzalez A, Hatt JK, Moe C, Kirby A, Konstantinidis KT. The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study. mBio 2020; 11:e02634-20. [PMID: 33203758 PMCID: PMC7683401 DOI: 10.1128/mbio.02634-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - A Peña-Gonzalez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - C Moe
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - A Kirby
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - K T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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88
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Guo M, Miao M, Wang Y, Duan M, Yang F, Chen Y, Yuan W, Zheng H. Developmental differences in the intestinal microbiota of Chinese 1-year-old infants and 4-year-old children. Sci Rep 2020; 10:19470. [PMID: 33173227 PMCID: PMC7656257 DOI: 10.1038/s41598-020-76591-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
The microbiota profile of children changes with age. To investigate the differences in the gut microbiota profile of 1- and 4-year-old children, we collected fecal samples and sequenced the V3-V4 hypervariable region of the 16S rRNA gene via high-throughput DNA sequencing. From phylum to species level, the microbiota underwent significant changes with age. The abundance of phyla Proteobacteria and Actinobacteria declined with age, whereas phyla Firmicutes and Bacteroidetes increased with age and dominated the gut microbiota of 4-year-olds. The intestinal environment of children at age four is closer to maturity. Hence, the abundance of Bifidobacterium significantly decreased in the gut of 4-year-olds, whereas Akkermansia muciniphila increased from 0.14% in 1-year-olds to 4.25% in 4-year-olds. The functional change in gut microbiota is consistent with changes in infant food, as microbiota participating in amino acid and vitamin metabolism were enriched in 1-year-olds, whereas microbiota involved in lipid metabolism increased with age.
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Affiliation(s)
- Min Guo
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China
| | - Maohua Miao
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Mengmeng Duan
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China
| | - Fen Yang
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China
| | - Yao Chen
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China
| | - Wei Yuan
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China.
| | - Huajun Zheng
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, 200032, China.
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Alauzet C, Cunat L, Wack M, Lanfumey L, Legrand-Frossi C, Lozniewski A, Agrinier N, Cailliez-Grimal C, Frippiat JP. Impact of a Model Used to Simulate Chronic Socio-Environmental Stressors Encountered during Spaceflight on Murine Intestinal Microbiota. Int J Mol Sci 2020; 21:ijms21217863. [PMID: 33114008 PMCID: PMC7672645 DOI: 10.3390/ijms21217863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
During deep-space travels, crewmembers face various physical and psychosocial stressors that could alter gut microbiota composition. Since it is well known that intestinal dysbiosis is involved in the onset or exacerbation of several disorders, the aim of this study was to evaluate changes in intestinal microbiota in a murine model used to mimic chronic psychosocial stressors encountered during a long-term space mission. We demonstrate that 3 weeks of exposure to this model (called CUMS for Chronic Unpredictable Mild Stress) induce significant change in intracaecal β-diversity characterized by an important increase of the Firmicutes/Bacteroidetes ratio. These alterations are associated with a decrease of Porphyromonadaceae, particularly of the genus Barnesiella, a major member of gut microbiota in mice and humans where it is described as having protective properties. These results raise the question of the impact of stress-induced decrease of beneficial taxa, support recent data deduced from in-flight experimentations and other ground-based models, and emphasize the critical need for further studies exploring the impact of spaceflight on intestinal microbiota in order to propose strategies to countermeasure spaceflight-associated dysbiosis and its consequences on health.
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Affiliation(s)
- Corentine Alauzet
- Stress Immunity Pathogens unit (SIMPA), EA 7300, Université de Lorraine, F-54000 Nancy, France; (L.C.); (C.L.-F.); (A.L.); (C.C.-G.); (J.-P.F.)
- CHRU-Nancy, Service de Microbiologie, F-54000 Nancy, France
- Correspondence: ; Tel.: +33-383-153-938
| | - Lisiane Cunat
- Stress Immunity Pathogens unit (SIMPA), EA 7300, Université de Lorraine, F-54000 Nancy, France; (L.C.); (C.L.-F.); (A.L.); (C.C.-G.); (J.-P.F.)
| | - Maxime Wack
- Département d’Informatique Médicale, Biostatistiques et Santé Publique, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France;
- Centre de Recherche des Cordeliers, INSERM, UMRS 1138, Université de Paris, 75006 Paris, France
| | - Laurence Lanfumey
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, F-75014 Paris, France;
| | - Christine Legrand-Frossi
- Stress Immunity Pathogens unit (SIMPA), EA 7300, Université de Lorraine, F-54000 Nancy, France; (L.C.); (C.L.-F.); (A.L.); (C.C.-G.); (J.-P.F.)
| | - Alain Lozniewski
- Stress Immunity Pathogens unit (SIMPA), EA 7300, Université de Lorraine, F-54000 Nancy, France; (L.C.); (C.L.-F.); (A.L.); (C.C.-G.); (J.-P.F.)
- CHRU-Nancy, Service de Microbiologie, F-54000 Nancy, France
| | - Nelly Agrinier
- CHRU-Nancy, INSERM, Université de Lorraine, CIC, Epidémiologie Clinique, F-54000 Nancy, France;
| | - Catherine Cailliez-Grimal
- Stress Immunity Pathogens unit (SIMPA), EA 7300, Université de Lorraine, F-54000 Nancy, France; (L.C.); (C.L.-F.); (A.L.); (C.C.-G.); (J.-P.F.)
| | - Jean-Pol Frippiat
- Stress Immunity Pathogens unit (SIMPA), EA 7300, Université de Lorraine, F-54000 Nancy, France; (L.C.); (C.L.-F.); (A.L.); (C.C.-G.); (J.-P.F.)
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Li Y, Zhu Y, Wei H, Chen Y, Shang H. Study on the Diversity and Function of Gut Microbiota in Pigs Following Long-Term Antibiotic and Antibiotic-Free Breeding. Curr Microbiol 2020; 77:4114-4128. [PMID: 33067706 DOI: 10.1007/s00284-020-02240-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 10/01/2020] [Indexed: 12/13/2022]
Abstract
In-feed antibiotics can influence intestinal microbial structures in born and early-life within a period. However, the impact of antibiotics on gut microbiota during long-term antibiotic-free and antibiotic breeding at porcine-fattening phase have not been studied extensively so far. Here, we conducted a systematic 16S rRNA gene sequencing-based study combined with metagenomic analysis to reveal the variation of diversity and function of gut microbiota between antibiotic-free (treatment group, TG) and antibiotic (a mixture of flavomycin and enramycin, control group, CG) breeding at various stages of fattening pigs. In the present study, Bacteroidetes, Firmicutes, and Proteobacteria phyla were the core microbiomes in fattening pig gut microbiota. The ratio between Firmicutes and Bacteroidetes significantly increased with age (P = 0.03). TG showed significantly higher relative abundance of Proteobacteria and Fibrobacteres phyla than CG. The microbial community can be divided into several notably clustered blocks based on cooperative and competitive correlations. These blocks centered on numerous special genera, which play essential roles in body development and disease prevention. TG showed obviously higher proportions of metabolic pathways related to metabolism, endocrine system, nervous system and excretory system, but pathways included carbohydrate metabolism and immune system diseases in CG. Collectively, this study has comprehensively demonstrated microbial diversities, differences and correlations among gut microbiota, microbial metabolism and gene functions during long-term antibiotic-free breeding. This work provides a novel resource and information with positive implications for pig husbandry production and disease prevention.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China
- Shenzhen Kingsino Technology Co., Ltd, Shenzhen, 518107, Guangdong, China
| | - Yuhua Zhu
- Shenzhen Kingsino Technology Co., Ltd, Shenzhen, 518107, Guangdong, China
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hong Wei
- Shenzhen Kingsino Technology Co., Ltd, Shenzhen, 518107, Guangdong, China
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China
| | - Haitao Shang
- Shenzhen Kingsino Technology Co., Ltd, Shenzhen, 518107, Guangdong, China.
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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91
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Castañeda S, Muñoz M, Villamizar X, Hernández PC, Vásquez LR, Tito RY, Ramírez JD. Microbiota characterization in Blastocystis-colonized and Blastocystis-free school-age children from Colombia. Parasit Vectors 2020; 13:521. [PMID: 33066814 PMCID: PMC7565366 DOI: 10.1186/s13071-020-04392-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/07/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Blastocystis is a protist that lives in the intestinal tract of a variety of hosts, including humans. It is still unclear how Blastocystis causes disease, which presents an ongoing challenge for researchers. Despite the controversial findings on the association between Blastocystis and clinical digestive manifestations, there is currently no consensus as to whether this protozoan actually behaves as a pathogen in humans. Furthermore, the relationship between Blastocystis and the intestinal microbiota composition is not yet clear. For that reason, the aim of this study was to identify if colonization by Blastocystis is related to changes in the diversity and relative abundance of bacterial communities, compared with those of Blastocystis-free individuals in a group of Colombian children. METHODS We took stool samples from 57 school-aged children attending a daycare institution in Popayán (Southwest Colombia). Whole DNA was extracted and examined by 16S-rRNA amplicon-based sequencing. Blastocystis was detected by real time PCR and other intestinal parasites were detected by microscopy. We evaluated if Blastocystis was associated with host variables and the diversity and abundance of microbial communities. RESULTS The composition of the intestinal bacterial community was not significantly different between Blastocystis-free and Blastocystis-colonized children. Despite this, we observed a higher microbial richness in the intestines of children colonized by Blastocystis, which could, therefore, be considered a benefit to intestinal health. The phylum Firmicutes was the predominant taxonomic unit in both groups analyzed. In Blastocystis-free individuals, there was a higher proportion of Bacteroidetes; similarly, in children colonized by Blastocystis, there was a higher relative abundance of the phylum Proteobacteria; however, no statistically significant differences were found between the comparison groups. CONCLUSIONS The presence of Blastocystis showed a decrease in Bacteroides, and an increase in the relative abundance of the genus Faecalibacterium. It was also evident that the presence of Blastocystis was unrelated to dysbiosis at the intestinal level; on the contrary, its presence did not show statistically differences in the intestinal microbiota composition. Nevertheless, we believe that Blastocystis plays a role in the ecology of the intestinal microbiota through its interaction with other microbial components.
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Affiliation(s)
- Sergio Castañeda
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Maestría en Informática Biomédica, Facultad de Medicina, Universidad El Bosque, Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Ximena Villamizar
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Paula C Hernández
- Laboratorio de Parasitología Molecular, Vicerrectoría de Investigaciones, Universidad El Bosque, Bogotá, Colombia
| | - Luis Reinel Vásquez
- Centro de Estudios en Microbiología y Parasitología (CEMPA), Departamento de Medicina Interna, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia
| | - Raúl Yhossef Tito
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, University of Leuven, Leuven, Belgium
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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Moossavi S, Atakora F, Fehr K, Khafipour E. Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota. BMC Microbiol 2020; 20:290. [PMID: 32948144 PMCID: PMC7501722 DOI: 10.1186/s12866-020-01949-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In recent years, the microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation based on sequence similarity to denoising algorithms that identify exact amplicon sequence variants (ASVs), and methods to identify contaminating bacterial DNA sequences from low biomass samples have been developed. Although these methods improve accuracy when analyzing mock communities, their impact on real samples and downstream analysis of biological associations is less clear. RESULTS Here, we re-processed our recently published milk microbiota data using Qiime1 to identify OTUs, and Qiime2 to identify ASVs, with or without contaminant removal using decontam. Qiime2 resolved the mock community more accurately, primarily because Qiime1 failed to detect Lactobacillus. Qiime2 also considerably reduced the average number of ASVs detected in human milk samples (364 ± 145 OTUs vs. 170 ± 73 ASVs, p < 0.001). Compared to the richness, the estimated diversity measures had a similar range using both methods albeit statistically different (inverse Simpson index: 14.3 ± 8.5 vs. 15.6 ± 8.7, p = 0.031) and there was strong consistency and agreement for the relative abundances of the most abundant bacterial taxa, including Staphylococcaceae and Streptococcaceae. One notable exception was Oxalobacteriaceae, which was overrepresented using Qiime1 regardless of contaminant removal. Downstream statistical analyses were not impacted by the choice of algorithm in terms of the direction, strength, and significance of associations of host factors with bacterial diversity and overall community composition. CONCLUSION Overall, the biological observations and conclusions were robust to the choice of the sequencing processing methods and contaminant removal.
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Affiliation(s)
- Shirin Moossavi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
- Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Winnipeg, MB, Canada.
- Present Address Department of Physiology and Pharmacology & Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada.
| | - Faisal Atakora
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Kelsey Fehr
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
- Present Address Microbiome Research and Technical Support, Cargill Animal Nutrition, Diamond V brand, Cedar Rapids, USA
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93
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Padayachee T, Nzuza N, Chen W, Nelson DR, Syed K. Impact of lifestyle on cytochrome P450 monooxygenase repertoire is clearly evident in the bacterial phylum Firmicutes. Sci Rep 2020; 10:13982. [PMID: 32814804 PMCID: PMC7438502 DOI: 10.1038/s41598-020-70686-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, are well known for their role in organisms' primary and secondary metabolism. Research on eukaryotes such as animals, plants, oomycetes and fungi has shown that P450s profiles in these organisms are affected by their lifestyle. However, the impact of lifestyle on P450 profiling in bacteria is scarcely reported. This study is such an example where the impact of lifestyle seems to profoundly affect the P450 profiles in the bacterial species belonging to the phylum Firmicutes. Genome-wide analysis of P450s in 972 Firmicutes species belonging to 158 genera revealed that only 229 species belonging to 37 genera have P450s; 38% of Bacilli species, followed by 14% of Clostridia and 2.7% of other Firmicutes species, have P450s. The pathogenic or commensal lifestyle influences P450 content to such an extent that species belonging to the genera Streptococcus, Listeria, Staphylococcus, Lactobacillus, Lactococcus and Leuconostoc do not have P450s, with the exception of a handful of Staphylococcus species that have a single P450. Only 18% of P450s are found to be involved in secondary metabolism and 89 P450s that function in the synthesis of specific secondary metabolites are predicted. This study is the first report on comprehensive analysis of P450s in Firmicutes.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa.
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Chaplin A, Gao H, Asase C, Rengasamy P, Park B, Skander D, Bebek G, Rajagopalan S, Maiseyeu A. Systemically-delivered biodegradable PLGA alters gut microbiota and induces transcriptomic reprogramming in the liver in an obesity mouse model. Sci Rep 2020; 10:13786. [PMID: 32796856 PMCID: PMC7429827 DOI: 10.1038/s41598-020-69745-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023] Open
Abstract
Biodegradable materials, including the widely used poly (lactic-co-glycolic acid) (PLGA) nanoparticles contained in slow-release drug formulations, scaffolds and implants, are ubiquitous in modern biomedicine and are considered inert or capable of being metabolized through intermediates such as lactate. However, in the presence of metabolic stress, such as in obesity, the resulting degradation products may play a detrimental role, which is still not well understood. We evaluated the effect of intravenously-administered PLGA nanoparticles on the gut-liver axis under conditions of caloric excess in C57BL/6 mice. Our results show that PLGA nanoparticles accumulate and cause gut acidification in the cecum, accompanied by significant changes in the microbiome, with a marked decrease of Firmicutes and Bacteroidetes. This was associated with transcriptomic reprogramming in the liver, with a downregulation of mitochondrial function, and an increase in key enzymatic, inflammation and cell activation pathways. No changes were observed in systemic inflammation. Metagenome analysis coupled with publicly available microarray data suggested a mechanism of impaired PLGA degradation and intestinal acidification confirming an important enterohepatic axis of metabolite-microbiome interaction resulting in maintenance of metabolic homeostasis. Thus, our results have important implications for the investigation of PLGA use in metabolically-compromised clinical and experimental settings.
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Affiliation(s)
- Alice Chaplin
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Huiyun Gao
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Courteney Asase
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Palanivel Rengasamy
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Bongsoo Park
- Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Danielle Skander
- Department of Nutrition, Department of Electrical Engineering and Computer Science, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Gürkan Bebek
- Department of Nutrition, Department of Electrical Engineering and Computer Science, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Sanjay Rajagopalan
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Andrei Maiseyeu
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
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Cesinger MR, Thomason MK, Edrozo MB, Halsey CR, Reniere ML. Listeria monocytogenes SpxA1 is a global regulator required to activate genes encoding catalase and heme biosynthesis enzymes for aerobic growth. Mol Microbiol 2020; 114:230-243. [PMID: 32255216 PMCID: PMC7496741 DOI: 10.1111/mmi.14508] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/24/2022]
Abstract
An imbalance of cellular oxidants and reductants causes redox stress, which must be rapidly detected to restore homeostasis. In bacteria, the Firmicutes encode conserved Spx-family transcriptional regulators that modulate transcription in response to redox stress. SpxA1 is an Spx-family orthologue in the intracellular pathogen Listeria monocytogenes that is essential for aerobic growth and pathogenesis. Here, we investigated the role of SpxA1 in growth and virulence by identifying genes regulated by SpxA1 in broth and during macrophage infection. We found SpxA1-activated genes encoding heme biosynthesis enzymes and catalase (kat) were required for L. monocytogenes aerobic growth in rich medium. An Spx-recognition motif previously defined in Bacillus subtilis was identified in the promoters of SpxA1-activated genes and proved necessary for the proper activation of two genes, indicating this regulation by SpxA1 is likely direct. Together, these findings elucidated the mechanism of spxA1 essentiality in vitro and demonstrated that SpxA1 is required for basal expression of scavenging enzymes to combat redox stress generated in the presence of oxygen.
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Affiliation(s)
- Monica R. Cesinger
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Maureen K. Thomason
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Mauna B. Edrozo
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Cortney R. Halsey
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Michelle L. Reniere
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
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96
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Guérin F, Lachaal S, Auzou M, Le Brun C, Barraud O, Decousser JW, Lienhard R, Baraduc R, Dubreuil L, Cattoir V. Molecular basis of macrolide-lincosamide-streptogramin (MLS) resistance in Finegoldia magna clinical isolates. Anaerobe 2020; 64:102220. [PMID: 32531434 DOI: 10.1016/j.anaerobe.2020.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Affiliation(s)
- François Guérin
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France; Université de Caen Normandie, EA4655 (équipe "Antibio-résistance"), Caen, F-14032, France
| | - Sabrine Lachaal
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France
| | - Michel Auzou
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France; Université de Caen Normandie, EA4655 (équipe "Antibio-résistance"), Caen, F-14032, France
| | - Cécile Le Brun
- CHRU de Tours, Service de Bactériologie-Virologie, Hôpital Bretonneau, F-37044, Tours, France
| | - Olivier Barraud
- CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, Limoges, F-87042, France
| | - Jean-Winoc Decousser
- CHU Henri Mondor, Assistance Publique-Hôpitaux de Paris, Laboratoire de Microbiologie, Créteil, F-94010, France
| | - Reto Lienhard
- ADMED Microbiologie, La-Chaux-de-Fonds, CH-2303, Switzerland
| | - Régine Baraduc
- CHU de Clermont-Ferrand, Laboratoire de Microbiologie, Clermont-Ferrand, F-63003, France
| | - Luc Dubreuil
- CHRU de Lille, Laboratoire de Bactériologie-Hygiène et de Virologie, Lille, F-59 037, France
| | - Vincent Cattoir
- CHU Rennes, Service de Bactériologie et Hygiène Hospitalière, Rennes, F-35033, France; CNR de la Résistance aux Antibiotiques, Rennes, F-35033, France.
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97
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Deb S, Das L, Das SK. Composition and functional characterization of the gut microbiome of freshwater pufferfish (Tetraodon cutcutia). Arch Microbiol 2020; 202:2761-2770. [PMID: 32737543 DOI: 10.1007/s00203-020-01997-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 11/26/2022]
Abstract
This study describes the community composition and functions of the gut microbiome of the freshwater omnivorous pufferfish based on metagenomic approach. Metagenome sequence data showed a dominance of the class Gammaproteobacteria followed by Fusobacteria, Actinobacteria, Anerolineae, Betaproteobacteria, Deinococci, Clostridia and Deltaproteobacteria. At the order level, the most abundant groups were Aeromonadales, Fusobacteriales, Enterobacterales, Synechococcales. The genus Aeromonas was the most predominant followed by Plesiomonas and Cetobacterium. Additionally, within the domain Archaea, class Methanomicrobia was most abundant followed by Hadesarchaea, Thermoplasmata, Candidatus Altiarchaeales, Candidatus Bathyarchaeota and Thermoprotei. The metabolic profile of the bacterial community exhibited a high prevalence of genes associated with core housekeeping functions, such as synthesis of cofactors, vitamins, prosthetic groups, pigments, amino acids and its derivatives, carbohydrate and protein metabolism. Comparative analysis with other fish gut microbiome showing similarity in protein metabolism with carnivorous Salmon and carbohydrate metabolism with herbivorous grass carp respectively. This study describes the bacterial community compositions are influenced by the trophic level.
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Affiliation(s)
- Sushanta Deb
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Lipika Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India.
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98
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Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA, Spicer D. Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study. Breast Cancer Res Treat 2020; 182:451-463. [PMID: 32468338 PMCID: PMC7297869 DOI: 10.1007/s10549-020-05702-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To investigate the association between gut microbiome with breast tumor characteristics (receptor status, stage and grade) and known breast cancer risk factors. METHODS In a pilot cross-sectional study of 37 incident breast cancer patients, fecal samples collected prior to chemotherapy were analyzed by 16S ribosomal RNA (rRNA) gene-based sequencing protocol. Alpha diversity and specific taxa by tumor characteristics and breast cancer risk factors were tested by Wilcoxon rank sum test, and by differential abundance analysis, using a zero-inflated negative binomial regression model with adjustment for total counts, age and race/ethnicity. RESULTS There were no significant alpha diversity or phyla differences by estrogen/progesterone receptor status, tumor grade, stage, parity and body mass index. However, women with human epidermal growth factor receptor 2 positive (HER2+) (n = 12) compared to HER2- (n = 25) breast cancer showed 12-23% lower alpha diversity [number of species (OTU) p = 0.033, Shannon index p = 0.034], lower abundance of Firmicutes (p = 0.005) and higher abundance of Bacteroidetes (p = 0.089). Early menarche (ages ≤ 11) (n = 11) compared with later menarche (ages ≥ 12) (n = 26) was associated with lower OTU (p = 0.036), Chao1 index (p = 0.020) and lower abundance of Firmicutes (p = 0.048). High total body fat (TBF) (> 46%) (n = 12) compared to lower (≤ 46%) TBF was also associated with lower Chao 1 index (p = 0.011). There were other significant taxa abundance differences by HER2 status, menarche age, as well as other tumor and breast cancer risk factors. CONCLUSIONS AND RELEVANCE Further studies are needed to identify characteristics of the human microbiome and the interrelationships between breast cancer hormone receptor status and established breast cancer risk factors.
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Affiliation(s)
- Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Rm 4443, Los Angeles, CA, 90089, USA.
| | - Chiuchen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Rm 4443, Los Angeles, CA, 90089, USA
| | - Cheryl Vigen
- Mrs. TH Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA
| | - Yang Yu
- Global Data Science and Analytics- Medical Device Division, Abbott Laboratories, Santa Clara, CA, USA
| | - Wendy Cozen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Rm 4443, Los Angeles, CA, 90089, USA
| | - Agustin A Garcia
- Hematology Oncology, Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Darcy Spicer
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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99
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Villar E, Cabrol L, Heimbürger-Boavida LE. Widespread microbial mercury methylation genes in the global ocean. Environ Microbiol Rep 2020. [PMID: 32090489 DOI: 10.1111/1758-5662229.12829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.
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Affiliation(s)
- Emilie Villar
- Aix Marseille Université, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
- Sorbonne Université, Université Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teissier, CS90074, Roscoff, 29688, France
| | - Léa Cabrol
- Aix Marseille Université, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
- Instituto de Ecologia y Biodiversidad, Departamento de Ciencias Ecologicas, Facultad de Ciencias, Universidad de Chile, Santiago de Chile, Chile
| | - Lars-Eric Heimbürger-Boavida
- Aix Marseille Université, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
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100
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Abstract
Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.
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Affiliation(s)
- Emilie Villar
- Aix Marseille Université, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
- Sorbonne Université, Université Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teissier, CS90074, Roscoff, 29688, France
| | - Léa Cabrol
- Aix Marseille Université, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
- Instituto de Ecologia y Biodiversidad, Departamento de Ciencias Ecologicas, Facultad de Ciencias, Universidad de Chile, Santiago de Chile, Chile
| | - Lars-Eric Heimbürger-Boavida
- Aix Marseille Université, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
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