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Amin A, Mekadim C, Modrackova N, Bolechova P, Mrazek J, Neuzil-Bunesova V. Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. Anim Microbiome 2024; 6:21. [PMID: 38698458 PMCID: PMC11064412 DOI: 10.1186/s42523-024-00311-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.
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Affiliation(s)
- Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Petra Bolechova
- Department of Ethology and Companion Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic.
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Decousser JW, Barbut F, Baron R, Parneix P, Lavigne T, Romano-Bertrand S, For The Scientific Committee Of The French Society For Hospital Hygiene And The National Reference Laboratory For. Comments on the tolerance of Clostridioides difficile spores to disinfection with sodium hypochlorite disinfectant. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 38771011 DOI: 10.1099/mic.0.001435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- J W Decousser
- Équipe Opérationnelle d'Hygiène, Hôpitaux Universitaires Henri-Mondor, Assistance Publique-Hôpitaux de Paris, UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Enva, USC ANSES, Créteil, France
| | - F Barbut
- National Reference Laboratory for Clostridioides difficile, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, 75012 Paris, France; Université Paris Cité, INSERM UMR-1139, 75006 Paris, France
| | - R Baron
- Service Hygiène Hospitalière, Pôle Recherche et Santé Publique, Centre Hospitalier Universitaire de Brest, Brest, France
| | - P Parneix
- Nouvelle Aquitaine Healthcare-Associated Infection Control Centre, Bordeaux University Hospital, Bordeaux, France
| | - T Lavigne
- Service d'Hygiène Hospitalière, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - S Romano-Bertrand
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, Hospital Hygiene and Infection Control Department, University Hospital of Montpellier, Montpellier, France
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Young SM, Woode RA, Williams EC, Ericsson AC, Clarke LL. Fecal dysbiosis and inflammation in intestinal-specific Cftr knockout mice on regimens preventing intestinal obstruction. Physiol Genomics 2024; 56:247-264. [PMID: 38073491 DOI: 10.1152/physiolgenomics.00077.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/26/2023] Open
Abstract
Chronic intestinal inflammation is a poorly understood manifestation of cystic fibrosis (CF), which may be refractory to ion channel CF transmembrane conductance regulator (CFTR) modulator therapy. People with CF exhibit intestinal dysbiosis, which has the potential for stimulating intestinal and systemic inflammation. CFTR is expressed in organ epithelia, leukocytes, and other tissues. Here, we investigate the contribution of intestinal epithelium-specific loss of Cftr [iCftr knockout (KO)] to dysbiosis and inflammation in mice treated with either of two antiobstructive dietary regimens necessary to maintain CF mouse models [polyethylene glycol (PEG) laxative or a liquid diet (LiqD)]. Feces collected from iCftr KO mice and their wild-type (WT) sex-matched littermates were used to measure fecal calprotectin to evaluate inflammation and to perform 16S rRNA sequencing to characterize the gut microbiome. Fecal calprotectin was elevated in iCftr KO relative to WT mice that consumed either PEG or LiqD. PEG iCftr KO mice did not show a change in α diversity versus WT mice but demonstrated a significant difference in microbial composition (β diversity) with included increases in the phylum Proteobacteria, the family Peptostreptococcaceae, four genera of Clostridia including C. innocuum, and the mucolytic genus Akkermansia. Fecal microbiome analysis of LiqD-fed iCftr KO mice showed both decreased α diversity and differences in microbial composition with increases in the Proteobacteria family Enterobacteriaceae, Firmicutes families Clostridiaceae and Peptostreptococcaceae, and enrichment of Clostridium perfringens, C. innocuum, C. difficile, mucolytic Ruminococcus gnavus, and reduction of Akkermansia. It was concluded that epithelium-specific loss of Cftr is a major driver of CF intestinal dysbiosis and inflammation with significant similarities to previous studies of pan Cftr KO mice.NEW & NOTEWORTHY Chronic intestinal inflammation is a manifestation of cystic fibrosis (CF), a disease caused by loss of the anion channel CF transmembrane conductance regulator (CFTR) that is expressed in many tissues. This study shows that intestinal epithelial cell-specific loss of CFTR [inducible Cftr knockout (KO)] in mice is sufficient to induce intestinal dysbiosis and inflammation. Experiments were performed on mice consuming two dietary regimens routinely used to prevent obstruction in CF mice.
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Affiliation(s)
- Sarah M Young
- College of Veterinary Medicine, University of Missouri Comparative Medicine Program, Columbia, Missouri, United States
| | - Rowena A Woode
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Estela C Williams
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Aaron C Ericsson
- College of Veterinary Medicine, University of Missouri Comparative Medicine Program, Columbia, Missouri, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
- College of Veterinary Medicine, University of Missouri Metagenomics Center, Columbia, Missouri, United States
| | - Lane L Clarke
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, United States
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Cai X, Peng Y, Yang G, Feng L, Tian X, Huang P, Mao Y, Xu L. Populational genomic insights of Paraclostridium bifermentans as an emerging human pathogen. Front Microbiol 2023; 14:1293206. [PMID: 38029151 PMCID: PMC10665999 DOI: 10.3389/fmicb.2023.1293206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Paraclostridium bifermentans (P.b) is an emerging human pathogen that is phylogenomically close to Paeniclostridium sordellii (P.s), while their populational genomic features and virulence capacity remain understudied. Here, we performed comparative genomic analyses of P.b and compared their pan-genomic features and virulence coding profiles to those of P.s. Our results revealed that P.b has a more plastic pangenome, a larger genome size, and a higher GC content than P.s. Interestingly, the P.b and P.s share similar core-genomic functions, but P.b encodes more functions in nutrient metabolism and energy conversion and fewer functions in host defense in their accessory-genomes. The P.b may initiate extracellular infection processes similar to those of P.s and Clostridium perfringens by encoding three toxin homologs (i.e., microbial collagenase, thiol-activated cytolysin, phospholipase C, which are involved in extracellular matrices degradation and membrane damaging) in their core-genomes. However, P.b is less toxic than the P.s by encoding fewer secretion toxins in the core-genome and fewer lethal toxins in the accessory-genome. Notably, P.b carries more toxins genes in their accessory-genomes, particularly those of plasmid origin. Moreover, three within-species and highly conserved plasmid groups, encoding virulence, gene acquisition, and adaptation, were carried by 25-33% of P.b strains and clustered by isolation source rather than geography. This study characterized the pan-genomic virulence features of P.b for the first time, and revealed that P. bifermentans is an emerging pathogen that can threaten human health in many aspects, emphasizing the importance of phenotypic and genomic characterizations of in situ clinical isolates.
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Affiliation(s)
- Xunchao Cai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yao Peng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Gongli Yang
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Lijuan Feng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Xiaojuan Tian
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Ping Huang
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Long Xu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong, China
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Young SM, Woode RA, Williams E, Ericsson A, Clarke LL. Fecal Dysbiosis and Inflammation in Intestinal-Specific Cftr Knockout Mice on Regimens Preventing Intestinal Obstruction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550378. [PMID: 37546931 PMCID: PMC10402002 DOI: 10.1101/2023.07.24.550378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Chronic intestinal inflammation is a poorly understood manifestation of Cystic Fibrosis (CF), which may be refractory to ion channel CFTR modulator therapy. People with CF exhibit intestinal dysbiosis which has potential for stimulating intestinal and systemic inflammation. CFTR is expressed in organ epithelia and in the leukocyte population. Here, we investigate the contribution of intestinal epithelial-specific loss of Cftr (iCftr KO) to dysbiosis and inflammation in mice treated with either of two anti-obstructive dietary regimens necessary to maintain CF mouse models (PEG laxative or a liquid diet, LiqD). Feces collected from iCftr KO mice and their wildtype (WT) sex-matched littermates were used to measure fecal calprotectin and to perform 16S rRNA sequencing to characterize the gut microbiome. Fecal calprotectin was elevated in iCftr KO relative to WT samples of mice consuming either PEG or LiqD. PEG iCftr KO mice did not show a change in α-diversity versus WT but demonstrated a significant difference in microbial composition (β-diversity) with increases in phylum Proteobacteria , family Peptostreptococcaceae , four genera of Clostridia including C. innocuum , and mucolytic genus Akkermansia . Fecal microbiome analysis of LiqD iCftr KO mice showed both decreased α-diversity and differences in microbial composition with increases in Proteobacteria family Enterobacteriaceae , Firmicutes families Clostridiaceae and Peptostreptococcaceae , and enrichment of Clostridium perfringens , C. innocuum , C. difficile , mucolytic Ruminococcus gnavus , and reduction of Akkermansia . It was concluded that epithelial-specific loss of Cftr is a major driver of CF intestinal dysbiosis and inflammation with significant similarities to previous studies of global Cftr KO mice. New and noteworthy Chronic intestinal inflammation is a manifestation of cystic fibrosis (CF), a disease caused by loss of the anion channel CFTR that is expressed in many tissues. This study shows that intestinal epithelial cell-specific loss of CFTR (iCftr KO) in mice is sufficient to induce intestinal dysbiosis and inflammation. Studies were performed on mice consuming either dietary regimen (PEG laxative or liquid diet) routinely used to prevent obstruction in CF mice.
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Roe JM, Seely K, Bussard CJ, Eischen Martin E, Mouw EG, Bayles KW, Hollingsworth MA, Brooks AE, Dailey KM. Hacking the Immune Response to Solid Tumors: Harnessing the Anti-Cancer Capacities of Oncolytic Bacteria. Pharmaceutics 2023; 15:2004. [PMID: 37514190 PMCID: PMC10384176 DOI: 10.3390/pharmaceutics15072004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Oncolytic bacteria are a classification of bacteria with a natural ability to specifically target solid tumors and, in the process, stimulate a potent immune response. Currently, these include species of Klebsiella, Listeria, Mycobacteria, Streptococcus/Serratia (Coley's Toxin), Proteus, Salmonella, and Clostridium. Advancements in techniques and methodology, including genetic engineering, create opportunities to "hijack" typical host-pathogen interactions and subsequently harness oncolytic capacities. Engineering, sometimes termed "domestication", of oncolytic bacterial species is especially beneficial when solid tumors are inaccessible or metastasize early in development. This review examines reported oncolytic bacteria-host immune interactions and details the known mechanisms of these interactions to the protein level. A synopsis of the presented membrane surface molecules that elicit particularly promising oncolytic capacities is paired with the stimulated localized and systemic immunogenic effects. In addition, oncolytic bacterial progression toward clinical translation through engineering efforts are discussed, with thorough attention given to strains that have accomplished Phase III clinical trial initiation. In addition to therapeutic mitigation after the tumor has formed, some bacterial species, referred to as "prophylactic", may even be able to prevent or "derail" tumor formation through anti-inflammatory capabilities. These promising species and their particularly favorable characteristics are summarized as well. A complete understanding of the bacteria-host interaction will likely be necessary to assess anti-cancer capacities and unlock the full cancer therapeutic potential of oncolytic bacteria.
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Affiliation(s)
- Jason M Roe
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Kevin Seely
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Caleb J Bussard
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80130, USA
| | | | - Elizabeth G Mouw
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Michael A Hollingsworth
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Amanda E Brooks
- College of Osteopathic Medicine, Rocky Vista University, Ivins, UT 84738, USA
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80130, USA
- Office of Research & Scholarly Activity, Rocky Vista University, Ivins, UT 84738, USA
| | - Kaitlin M Dailey
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Guo K, Figueroa-Romero C, Noureldein M, Hinder LM, Sakowski SA, Rumora AE, Petit H, Savelieff MG, Hur J, Feldman EL. Gut microbiota in a mouse model of obesity and peripheral neuropathy associated with plasma and nerve lipidomics and nerve transcriptomics. MICROBIOME 2023; 11:52. [PMID: 36922895 PMCID: PMC10015923 DOI: 10.1186/s40168-022-01436-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Peripheral neuropathy (PN) is a common complication in obesity, prediabetes, and type 2 diabetes, though its pathogenesis remains incompletely understood. In a murine high-fat diet (HFD) obesity model of PN, dietary reversal (HFD-R) to a low-fat standard diet (SD) restores nerve function and the nerve lipidome to normal. As the gut microbiome represents a potential link between dietary fat intake and nerve health, the current study assessed shifts in microbiome community structure by 16S rRNA profiling during the paradigm of dietary reversal (HFD-R) in various gut niches. Dietary fat content (HFD versus SD) was also correlated to gut flora and metabolic and PN phenotypes. Finally, PN-associated microbial taxa that correlated with the plasma and sciatic nerve lipidome and nerve transcriptome were used to identify lipid species and genes intimately related to PN phenotypes. RESULTS Microbiome structure was altered in HFD relative to SD but rapidly reversed with HFD-R. Specific taxa variants correlating positively with metabolic health associated inversely with PN, while specific taxa negatively linked to metabolic health positively associated with PN. In HFD, PN-associated taxa variants, including Lactobacillus, Lachnoclostridium, and Anaerotruncus, also positively correlated with several lipid species, especially elevated plasma sphingomyelins and sciatic nerve triglycerides. Negative correlations were additionally present with other taxa variants. Moreover, relationships that emerged between specific PN-associated taxa variants and the sciatic nerve transcriptome were related to inflammation, lipid metabolism, and antioxidant defense pathways, which are all established in PN pathogenesis. CONCLUSIONS The current results indicate that microbiome structure is altered with HFD, and that certain taxa variants correlate with metabolic health and PN. Apparent links between PN-associated taxa and certain lipid species and nerve transcriptome-related pathways additionally provide insight into new targets for microbiota and the associated underlying mechanisms of action in PN. Thus, these findings strengthen the possibility of a gut-microbiome-peripheral nervous system signature in PN and support continuing studies focused on defining the connection between the gut microbiome and nerve health to inform mechanistic insight and therapeutic opportunities. Video Abstract.
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Affiliation(s)
- Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Mohamed Noureldein
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Lucy M. Hinder
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
- Reata Pharmaceuticals, Irving, TX 75063 USA
| | - Stacey A. Sakowski
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Amy E. Rumora
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Neurology, Columbia University, New York, NY 10032 USA
| | - Hayley Petit
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Masha G. Savelieff
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Junguk Hur
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202 USA
| | - Eva L. Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA
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Shang Z, Wang Y, An M, Chen X, Kulyar MFEA, Tan Z, Liu S, Li K. The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks’ excrement contamination in plateau, China. Front Microbiol 2022; 13:1016852. [DOI: 10.3389/fmicb.2022.1016852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (>3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.
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Zhou Y, Wang S, Weng XB. Clostridium subterminale infection in a patient with diffuse large B-cell lymphoma and haemophagocytic syndrome: A case report and literature review. J Int Med Res 2022; 50:3000605221129558. [PMID: 36217260 PMCID: PMC9558875 DOI: 10.1177/03000605221129558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Although uncommon, infection caused by Clostridium subterminale
may be life threatening particularly in immunocompromised patients. We report
here a rare presentation of a patient with diffuse large B-cell lymphoma and
haemophagocytic syndrome associated with C. subterminale
bacteraemia. The management of the patient is described as well as a review of
medical literature. Infection by Clostridium species, including
C. subterminale, should be considered in a febrile patient
with a haematologic malignancy. The case highlights the importance of using gene
sequencing for identification of this anaerobic organism.
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Affiliation(s)
- Ying Zhou
- School of Medicine, Ningbo University, Ningbo, China,Birth Defects Prevention Laboratory, Ningbo Women's and
Children's Hospital, Ningbo, China
| | - Sheng Wang
- Department of Medical Laboratory, Ningbo First Hospital, Ningbo,
China
| | - Xing-bei Weng
- Department of Medical Laboratory, Ningbo First Hospital, Ningbo,
China,Xing-bei Weng, Guangji Street 31, Haishu
District, Ningbo 315010, China.
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10
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Schnizlein MK, Young VB. Capturing the environment of the Clostridioides difficile infection cycle. Nat Rev Gastroenterol Hepatol 2022; 19:508-520. [PMID: 35468953 DOI: 10.1038/s41575-022-00610-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/11/2022]
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection is a substantial health and economic burden worldwide. Great strides have been made over the past several years in characterizing the physiology of C. difficile infection, particularly regarding how gut microorganisms and their host work together to provide colonization resistance. As mammalian hosts and their indigenous gut microbiota have co-evolved, they have formed a complex yet stable relationship that prevents invading microorganisms from establishing themselves. In this Review, we discuss the latest advances in our understanding of C. difficile physiology that have contributed to its success as a pathogen, including its versatile survival factors and ability to adapt to unique niches. Using discoveries regarding microorganism-host and microorganism-microorganism interactions that constitute colonization resistance, we place C. difficile within the fiercely competitive gut environment. A comprehensive understanding of these relationships is required to continue the development of precision medicine-based treatments for C. difficile infection.
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Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
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11
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Ren L, Ma XL, Wang HL, Li R, Cui JJ, Yan PJ, Wang YN, Yu XY, Du P, Yu HY, Guo HH, Tang R, Che YS, Zheng WS, Jiang JD, Wang LL. Prebiotic-like cyclodextrin assisted silybin on NAFLD through restoring liver and gut homeostasis. J Control Release 2022; 348:825-840. [PMID: 35752255 DOI: 10.1016/j.jconrel.2022.06.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with no currently approved treatment. The natural compound silybin (SLN) has versatile hepatoprotective efficacy with negligible adverse effects; however, poor absorption limits its clinical applications. Gut microbiota has been proposed to play a crucial role in the pathophysiology of NAFLD and targeted for disease control. Cyclodextrins, the cyclic oligosaccharides, were documented to have various health benefits with potential prebiotic properties. This study aimed to develop a silybin-2-hydroxypropyl-β-cyclodextrin inclusion (SHβCD) to improve the therapeutic efficacy of SLN and elucidate the mechanisms of improvement. The results showed that SLN formed a 1:1 stoichiometric inclusion complex with HP-β-CD. The solubility of SLN was increased by generating SHβCD, resulting in improved drug permeability and bioavailability. In high-fat diet (HFD)-fed hamsters, SHβCD modulated gut health by restoring the gut microbiota and intestinal integrity. SHβCD showed superior anti-lipid accumulation, antioxidant, and anti-inflammatory effects compared with SLN alone. Transcriptome analysis in the liver tissue implied that the improved inflammation and/or energy homeostasis was the potential mechanism. Therefore, SHβCD may be a promising alternative for the treatment of NAFLD, attributing to the dual functions of HβCD on drug absorption and gut microbial homeostasis.
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Affiliation(s)
- Ling Ren
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Xiao-Lei Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Hong-Liang Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Rui Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Jin-Jin Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Peng-Ju Yan
- JiaMuSi University, Heilongjiang 154007, China
| | - Ya-Nan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Xiao-You Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Peng Du
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Hao-Yang Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Hui-Hui Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Rou Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yong-Sheng Che
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Wen-Sheng Zheng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Jian-Dong Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Lu-Lu Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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Impact of the Gram-Negative-Selective Inhibitor MAC13243 on In Vitro Simulated Gut Microbiota. Pharmaceuticals (Basel) 2022; 15:ph15060731. [PMID: 35745650 PMCID: PMC9229071 DOI: 10.3390/ph15060731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
New Gram-negative-selective antimicrobials are desirable to avoid perturbations in the gut microbiota leading to antibiotic-induced dysbiosis. We investigated the impact of a prototype drug (MAC13243) interfering with the Gram-negative outer membrane protein LolA on the faecal microbiota. Faecal suspensions from two healthy human donors were exposed to MAC13243 (16, 32, or 64 mg/L) using an in vitro gut model (CoMiniGut). Samples collected 0, 4, and 8 h after exposure were subjected to viable cell counts, 16S rRNA gene quantification and V3-V4 sequencing using the Illumina MiSeq platform. MAC13243 exhibited concentration-dependent killing of coliforms in both donors after 8 h. Concentrations of ≤32 mg/L reduced the growth of aerobic bacteria without influencing the microbiota composition and diversity. An expansion of Firmicutes at the expense of Bacteroidetes and Actinobacteria was observed in the faecal microbiota from one donor following exposure to 64 mg/L of MAC13242. At all concentrations tested, MAC13243 did not lead to the proliferation of Escherichia coli nor a reduced abundance of beneficial bacteria, which are typical changes observed in antibiotic-induced dysbiosis. These results support our hypothesis that a drug interfering with a specific target in Gram-negative bacteria has a low impact on the commensal gut microbiota and, therefore, a low risk of inducing dysbiosis.
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Kunaseth J, Waiyaput W, Chanchaem P, Sawaswong V, Permpech R, Payungporn S, Sophonsritsuk A. Vaginal microbiome of women with adenomyosis: A case-control study. PLoS One 2022; 17:e0263283. [PMID: 35171931 PMCID: PMC8849446 DOI: 10.1371/journal.pone.0263283] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 01/16/2022] [Indexed: 01/02/2023] Open
Abstract
Immune dysregulation can involve invasion and survival of endometrial glands inside the myometrium of the adenomyosis. There is limited available data concerning alterations of the bacterial microbiome in the reproductive tract of adenomyosis women. The present cross-sectional age-matched study aims to compare vaginal microbiota between women with and without adenomyosis. We recruited women with adenomyosis (N = 40) and age-matched women without adenomyosis (N = 40) from the Departments of Obstetrics and Gynaecology, Ramathibodi Hospital Mahidol University, from August 2020 to January 2021. Vaginal swab samples were collected from the participants. DNA isolation and bacterial 16s rDNA gene sequencing and data analyses were then performed. Comparison of the diversity of vaginal microbiota, microbiota composition, and the operational taxonomic unit (OTU) between adenomyosis and non-adenomyosis (control) groups were undertaken. Data from 40 and 38 women with and without adenomyosis, respectively, were analyzed. Alpha-diversity analysis (Chao1 index) at the species level showed higher vaginal microbial richness in the adenomyosis group when compared with the control group (p = 0.006). The linear discriminant analysis effect size technique (LeFSe) indicated an elevated abundance of several vaginal microbial taxa in the adenomyosis group, including Alloscardovia, Oscillospirales, Ruminoccoccaceae, UCG_002, Oscillospiraceae, Enhydrobacter, Megamonas, Moraxellaceae, Subdoligranulum, Selenomonadaceae, and Faecalibacterium. On the other hand, an increase in the abundance of Megaspehera, Fastidiosipila, Hungateiclostridiaceae, and Clostridia was identified in the control group. Vaginal community state type (CST)-III and -IV were dominated in adenomyosis, while only CST-IV was dominated in the non-adenomyosis group. Lactobacillus was the most abundant vaginal microbial in both groups. In this study, the differences in vaginal microbiome profile were noted between adenomyosis and non-adenomyosis group. The increasing of microbial richness was associated with adenomyosis. Nevertheless, further investigations were required to elucidate the mechanisms and apply them for clinical implications.
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Affiliation(s)
- Jitsupa Kunaseth
- Reproductive Endocrinology and Infertility Unit, Department of Obstetrics and Gynaecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wanwisa Waiyaput
- Office of Research Academic and Innovation, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Vorthon Sawaswong
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Rattana Permpech
- Perioperative Nursing Division, Department of Ramathibodi Nursing Service, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (AS); (SP)
| | - Areepan Sophonsritsuk
- Reproductive Endocrinology and Infertility Unit, Department of Obstetrics and Gynaecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- * E-mail: (AS); (SP)
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Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genomics 2021; 113:4196-4205. [PMID: 34780936 DOI: 10.1016/j.ygeno.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspective, we have intensively analyzed its genomic and metabolic characteristics to comprehend the evolutionary conservation of amino acid catabolism by a comparative genomic approach. The whole-genome data indicated that CST has shown a phylogenomic similarity with hyper-ammonia producing, purinolytic, and proteolytic pathogenic Clostridia. CST has shown to common genomic context sharing across the purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genome syntenic analysis described that syntenic orthologs might be originated from the recent ancestor at a slow evolution rate and syntenic-out paralogs evolved from either CDF or CAC via α-event and β-event. Collinearity of either gene orders or gene families was adjusted with syntenic out-paralogs across these genomes. The genome-wide metabolic analysis predicted 11 unique putative metabolic subsystems from the CST genome for amino acid catabolism and hydrogen production. The in silico analysis of our study revealed that a characteristic system for amino acid catabolism-directed biofuel synthesis might have slowly evolved and established as a core genomic content of CST.
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Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland. Microorganisms 2020; 8:microorganisms8101604. [PMID: 33081036 PMCID: PMC7603099 DOI: 10.3390/microorganisms8101604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, one can expect the presence of distinct microbiomes across different CW zones. Here, we investigated spatial changes in microbiomes along different functional zones of a free-water surface wetland located in Moscow, Russia. The microbiome structure was analyzed using Illumina MiSeq amplicon sequencing. We also determined particle diameter and surface area of sediments, as well as chemical composition of organic pollutants in different CW zones. Specific organic particle aggregates similar to activated sludge flocs were identified in the sediments. The highest accumulation of hydrocarbons was found in the zones with predominant sedimentation of fine fractions. Phytofilters had the highest rate of organic pollutants decomposition and predominance of Smithella, Ignavibacterium, and Methanothrix. The sedimentation tank had lower microbial diversity, and higher relative abundances of Parcubacteria, Proteiniclasticum, and Macellibacteroides, as well as higher predicted abundances of genes related to methanogenesis and methanotrophy. Thus, spatial changes in microbiomes of constructed wetlands can be associated with different types of wastewater treatment processes.
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