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Heng YC, Kittelmann S. Proposal for reclassification of the species Hungatella xylanolytica as Lacrimispora xylanisolvens nom. nov. and transfer of the genus Hungatella to the family Lachnospiraceae. Int J Syst Evol Microbiol 2024; 74. [PMID: 38869948 DOI: 10.1099/ijsem.0.006417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
Hungatella xylanolytica X5-1T is an anaerobic, xylan-fermenting bacterium first isolated from methane-producing cattle manure. Initially identified as Bacteroides xylanolyticus, this species was later reclassified as H. xylanolytica in 2019. Although this reclassification found support through Genome blast Distance Phylogeny analysis which placed H. xylanolytica X5-1T into the same clade as Hungatella effluvii DSM 24995T, it was contradicted by 16S rRNA gene phylogenetic analysis, which associated it with a set of misnamed Clostridium species later reassigned into the genus Lacrimispora. To ascertain its taxonomic position, comparative analyses were performed to re-examine the relationship between H. xylanolytica X5-1T and all species of the genera Hungatella and Lacrimispora. The ranges of 16S rRNA gene sequence similarity, average amino acid identity, and percentage of conserved protein prediction values were higher between H. xylanolytica X5-1T and species of the genus Lacrimispora than Hungatella. In addition, H. xylanolytica X5-1T was found to harbour genes and pathways conserved and exclusive to species within the genus Lacrimispora but not Hungatella. Essentially, in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree, H. xylanolytica X5-1T clustered into the same clade as species of the genus Lacrimispora, distinct from species of the genus Hungatella. It is thus clear that H. xylanolytica X5-1T represents a species within the genus Lacrimispora, which we propose to reclassify as Lacrimispora xylanisolvens nom. nov. Finally, based on the results from the phylogenetic and comparative analyses, the genus Hungatella was transferred to the family Lachnospiraceae.
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Affiliation(s)
- Yu Chyuan Heng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
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Bou Sanayeh E, Tawfik M, Makram M, Khattar G, Qaqish F, Acharya S, Farag J, Chalhoub M, Glaser A. Hungatella hathewayi bacteremia due to acute appendicitis: A case report and a narrative review. Anaerobe 2024; 86:102838. [PMID: 38521228 DOI: 10.1016/j.anaerobe.2024.102838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Hungatella species, including Hungatella hathewayi and Hungatella effluvii, previously identified as part of the Clostridium genus, are anaerobic bacteria primarily residing in the gut microbiome, with infrequent implications in human infections. This article presents the case of an 87-year-old Asian male admitted for a hyperosmolar hyperglycemic state with septic shock secondary to Hungatella hathewayi bacteremia originating from acute appendicitis. Remarkably, the bacterium was detected in the blood 48 hours before the emergence of clinical and radiographic evidence of acute appendicitis. Additionally, we conducted a literature review to identify all documented human infections caused by Hungatella species. Timely microbial identification in such cases is essential for implementing targeted antibiotic therapy and optimizing clinical outcomes.
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Affiliation(s)
- Elie Bou Sanayeh
- Department of Internal Medicine, Staten Island University Hospital/Northwell Health, 475 Seaview Ave, Staten Island, NY, USA.
| | - Mark Tawfik
- Department of Internal Medicine, Staten Island University Hospital/Northwell Health, 475 Seaview Ave, Staten Island, NY, USA
| | - Marina Makram
- Touro College of Osteopathic Medicine, Harlem, NY, USA
| | - Georges Khattar
- Department of Internal Medicine, Staten Island University Hospital/Northwell Health, 475 Seaview Ave, Staten Island, NY, USA
| | - Faris Qaqish
- Department of Internal Medicine, Staten Island University Hospital/Northwell Health, 475 Seaview Ave, Staten Island, NY, USA
| | - Sudeep Acharya
- Department of Pulmonary and Critical Care, Staten Island University Hospital/Northwell Health, Staten Island, NY, USA
| | - Janet Farag
- Lake Erie College of Osteopathic Medicine, Bradenton, Florida, USA
| | - Michel Chalhoub
- Department of Pulmonary and Critical Care, Staten Island University Hospital/Northwell Health, Staten Island, NY, USA
| | - Allison Glaser
- Department of Infectious Diseases, Staten Island University Hospital/Northwell Health, Staten Island, NY, USA
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Maes M, Vasupanrajit A, Jirakran K, Klomkliew P, Chanchaem P, Tunvirachaisakul C, Plaimas K, Suratanee A, Payungporn S. Adverse childhood experiences and reoccurrence of illness impact the gut microbiome, which affects suicidal behaviours and the phenome of major depression: towards enterotypic phenotypes. Acta Neuropsychiatr 2023; 35:328-345. [PMID: 37052305 DOI: 10.1017/neu.2023.21] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The first publication demonstrating that major depressive disorder (MDD) is associated with alterations in the gut microbiota appeared in 2008 (Maes et al., 2008). The purpose of the present study is to delineate a) the microbiome signature of the phenome of depression, including suicidal behaviours (SB) and cognitive deficits; the effects of adverse childhood experiences (ACEs) and recurrence of illness index (ROI) on the microbiome; and the microbiome signature of lowered high-density lipoprotein cholesterol (HDLc). We determined isometric log-ratio abundances or prevalences of gut microbiome phyla, genera, and species by analysing stool samples from 37 healthy Thai controls and 32 MDD patients using 16S rDNA sequencing. Six microbiome taxa accounted for 36% of the variance in the depression phenome, namely Hungatella and Fusicatenibacter (positive associations) and Butyricicoccus, Clostridium, Parabacteroides merdae, and Desulfovibrio piger (inverse association). This profile (labelled enterotype 1) indicates compositional dysbiosis, is strongly predicted by ACE and ROI, and is linked to SB. A second enterotype was developed that predicted a decrease in HDLc and an increase in the atherogenic index of plasma (Bifidobacterium, P. merdae, and Romboutsia were positively associated, while Proteobacteria and Clostridium sensu stricto were negatively associated). Together, enterotypes 1 and 2 explained 40.4% of the variance in the depression phenome, and enterotype 1 in conjunction with HDLc explained 39.9% of the variance in current SB. In conclusion, the microimmuneoxysome is a potential new drug target for the treatment of severe depression and SB and possibly for the prevention of future episodes.
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Affiliation(s)
- Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul02447, Korea
- Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria
- IMPACT Strategic Research Center, Barwon Health, Geelong, Australia
| | - Asara Vasupanrajit
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Ketsupar Jirakran
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
- Maximizing Thai Children's Developmental Potential Research Unit, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pavit Klomkliew
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Prangwalai Chanchaem
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chavit Tunvirachaisakul
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Kitiporn Plaimas
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok, Bangkok10800, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Gryaznova M, Smirnova Y, Burakova I, Syromyatnikov M, Chizhkov P, Popov E, Popov V. Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10111-4. [PMID: 37365419 DOI: 10.1007/s12602-023-10111-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.
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Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036, Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018, Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036, Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018, Voronezh, Russia
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036, Voronezh, Russia
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036, Voronezh, Russia.
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018, Voronezh, Russia.
| | - Pavel Chizhkov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018, Voronezh, Russia
| | - Evgeny Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036, Voronezh, Russia
| | - Vasily Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036, Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018, Voronezh, Russia
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Munley JA, Nagpal R, Hanson NC, Mirzaie A, Laquian L, Mohr AM, Efron PA, Arnaoutakis DJ, Cooper MA. Chronic Mesenteric Ischemia Intestinal Dysbiosis Resolves after Revascularization. J Vasc Surg Cases Innov Tech 2022; 9:101084. [PMID: 36970136 PMCID: PMC10033993 DOI: 10.1016/j.jvscit.2022.101084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022] Open
Abstract
Objective Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mortality. Most of the perioperative morbidity has been secondary to postoperative multiple organ dysfunction, potentially from ischemia-reperfusion injury. The intestinal microbiome is a dense community of microorganisms in the gastrointestinal tract that help regulate pathways ranging from nutritional metabolism to the immune response. We hypothesized that patients with CMI will have microbiome perturbations that contribute to this inflammatory response and could potentially normalize in the postoperative period. Methods We performed a prospective study of patients with CMI who had undergone mesenteric bypass and/or stenting from 2019 to 2020. Stool samples were collected at three time points: preoperatively at the clinic, perioperatively within 14 days after surgery, and postoperatively at the clinic at >30 days after revascularization. Stool samples from healthy controls were used for comparison. The microbiome was measured using 16S rRNA sequencing on an Illumina-MiSeq sequence platform and analyzed using the QIIME2 (quantitative insights into microbial ecology 2)-DADA2 bioinformatics pipeline with the Silva database. Beta-diversity was analyzed using a principal coordinates analysis and permutational analysis of variance. Alpha-diversity (microbial richness and evenness) was compared using the nonparametric Mann-Whitney U test. Microbial taxa unique to CMI patients vs controls were identified using linear discriminatory analysis effect size analysis. P < .05 was considered statistically significant. Results Eight patients with CMI had undergone mesenteric revascularization (25% men; average age, 71 years). Nine healthy controls were also analyzed (78% men; average age, 55 years). Bacterial alpha-diversity (number of operational taxonomic units) was dramatically reduced preoperatively compared with that of the controls (P = .03). However, revascularization partially restored the species richness and evenness in the perioperative and postoperative phases. Beta-diversity was only different between the perioperative and postoperative groups (P = .03). Further analyses revealed increased abundance of Bacteroidetes and Clostridia taxa preoperatively and perioperatively compared with the controls, which was reduced during the postoperative period. Conclusions The results from the present study have shown that patients with CMI have intestinal dysbiosis that resolves after revascularization. The intestinal dysbiosis is characterized by the loss of alpha-diversity, which is restored perioperatively and maintained postoperatively. This microbiome restoration demonstrates the importance of intestinal perfusion to sustain gut homeostasis and suggests that microbiome modulation could be a possible intervention to ameliorate acute and subacute postoperative outcomes in these patients.
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Freitas RGBON, Vasques ACJ, Fernandes GR, Ribeiro FB, Solar I, Barbosa MG, Almeida-Pititto B, Geloneze B, Ferreira SRG. Gestational weight gain and visceral adiposity in adult offspring: Is there a link with the fecal abundance of Acidaminococcus genus? Eur J Clin Nutr 2022; 76:1705-1712. [PMID: 35906333 DOI: 10.1038/s41430-022-01182-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 11/08/2022]
Abstract
Intrauterine environment can influence the offspring's body adiposity whose distribution affect the cardiometabolic risk. Underlying mechanisms may involve the gut microbiome. We investigated associations of gestational weight gain with the adult offspring's gut microbiota, body adiposity and related parameters in participants of the Nutritionists' Health Study. METHODS This cross-sectional analysis included 114 women who had early life and clinical data, body composition, and biological samples collected. The structure of fecal microbiota was analyzed targeting the V4 region of the 16 S rRNA gene. Beta diversity was calculated by PCoA and PERMANOVA used to test the impact of categorical variables into the diversity. Bacterial clusters were identified based on the Jensen-Shannon divergence matrix and Calinski-Harabasz index. Correlations were tested by Spearman coefficient. RESULTS Median age was 28 (IQR 24-31) years and BMI 24.5 (IQR 21.4-28.0) kg/m2. Fifty-eight participants were assigned to a profile driven by Prevotella and 56 to another driven by Blautia. Visceral adipose tissue was correlated to abundance of Acidaminococcus genus considering the entire sample (r = 0.37; p < 0.001) and the profiles (Blautia: r = 0.35, p = 0.009, and Prevotella: r = 0.38, p = 0.006). In Blautia-driven profile, the same genus was also correlated to maternal gestational weight gain (r = 0.38, p = 0.006). CONCLUSIONS Association of Acidaminococcus with gestational weight gain could reinforce the relevance with mothers' nutritional status for gut colonization at the beginning of life. Whether Acidaminococcus abundance could be a marker for central distribution of adiposity in young women requires further investigation.
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Affiliation(s)
- R G B O N Freitas
- Department of Epidemiology, School of Public Health, University of São Paulo, São Paulo, Brazil
- Laboratory of Investigation in Metabolism and Diabetes, Gastrocentro, School of Medical Sciences - University of Campinas, São Paulo, Brazil
| | - A C J Vasques
- Laboratory of Investigation in Metabolism and Diabetes, Gastrocentro, School of Medical Sciences - University of Campinas, São Paulo, Brazil
- School of Applied Sciences - University of Campinas, São Paulo, Brazil
| | - G R Fernandes
- Oswaldo Cruz Foundation, Belo Horizonte, São Paulo, Brazil
| | - F B Ribeiro
- Laboratory of Investigation in Metabolism and Diabetes, Gastrocentro, School of Medical Sciences - University of Campinas, São Paulo, Brazil
| | - I Solar
- Laboratory of Investigation in Metabolism and Diabetes, Gastrocentro, School of Medical Sciences - University of Campinas, São Paulo, Brazil
- School of Applied Sciences - University of Campinas, São Paulo, Brazil
| | - M G Barbosa
- School of Applied Sciences - University of Campinas, São Paulo, Brazil
| | - B Almeida-Pititto
- Department of Preventive Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - B Geloneze
- Laboratory of Investigation in Metabolism and Diabetes, Gastrocentro, School of Medical Sciences - University of Campinas, São Paulo, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, São Paulo, Brazil
| | - S R G Ferreira
- Department of Epidemiology, School of Public Health, University of São Paulo, São Paulo, Brazil.
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Urvashi, Gundawar K, Sharma S, Choksket S, Sharma M, Grover V, Patil PB, Korpole S. Lacrimispora defluvii PI-S10-B5AT sp. nov., an Obligate Anaerobe, Isolated from an Industrial Waste and Reclassification of Hungatella xylanolytica as Lacrimispora xylanolytica and Clostridium indicum as Lacrimispora indica Comb. nov. Curr Microbiol 2022; 79:397. [DOI: 10.1007/s00284-022-03096-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
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Du C, Zhou X, Zhang K, Huang S, Wang X, Zhou S, Chen Y. Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep. BMC Microbiol 2022; 22:273. [DOI: 10.1186/s12866-022-02687-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Myostatin (MSTN) negatively regulates the muscle growth in animals and MSTN deficient sheep have been widely reported previously. The goal of this study was to explore how MSTN inactivation influences their gut microbiota composition and potential functions.
Results
We compared the slaughter parameters and meat quality of 3 MSTN-edited male sheep and 3 wild-type male sheep, and analyzed the gut microbiome of the MSTN-edited sheep (8 female and 8 male sheep) and wild-type sheep (8 female and 8 male sheep) through metagenomic sequencing. The results showed that the body weight, carcass weight and eye muscle area of MSTN-edited sheep were significantly higher, but there were no significant differences in the meat quality indexes. At the microbial level, the alpha diversity was significantly higher in the MSTN-edited sheep (P < 0.05), and the microbial composition was significantly different by PCoA analysis in the MSTN-edited and wild-type sheep. The abundance of Firmicutes significantly increased and Bacteroidota significantly decreased in the MSTN-edited sheep. At genus level, the abundance of Flavonifractor, Subdoligranulum, Ruthenibacterium, Agathobaculum, Anaerotignum, Oribacterium and Lactobacillus were significantly increased in the MSTN-edited sheep (P < 0.05). Further analysis of functional differences was found that the carotenoid biosynthesis was significantly increased and the peroxisome, apoptosis, ferroptosis, N-glycan biosynthesis, thermogenesis, and adipocytokines pathways were decreased in the MSTN-edited sheep (P < 0.05). Moreover, carbohydrate-active enzymes (CAZymes) results certified the abundance of the GH13_39, GH4, GH137, GH71 and PL17 were upregulated, and the GT41 and CBM20 were downregulated in the MSTN-edited sheep (P < 0.05).
Conclusions
Our study suggested that MSTN inactivation remarkably influenced the composition and potential function of hindgut microbial communities of the sheep, and significantly promoted growth performance without affecting meat quality.
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Tang T, Chen Y, Liu M, Du Y, Tan Y. Effect of pH on the performance of hydrogen production by dark fermentation coupled denitrification. ENVIRONMENTAL RESEARCH 2022; 208:112663. [PMID: 34995549 DOI: 10.1016/j.envres.2021.112663] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/15/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
High concentration nitrogen-containing organic wastewater is a potential substrate for hydrogen production by dark fermentation. In this study, the effect of initial pH on the performance of hydrogen production by dark fermentation coupled denitrification was investigated. The hydrogen production, liquid metabolites, nitrate, nitrite and microbial community were monitored under the condition of pH varying from 4 to 11. Results showed that the highest hydrogen production (70.94 ± 4.750 mL/g VSS), chemical oxygen demand (COD) removal rate (37.13 ± 1.86%) and nitrate reduction rate (1.57 ± 0.27 mg/L/h) were obtained at pH of 5. Under this condition, the nitrate was mainly reduced to N2 with hydrogen as the electron donor. When the initial pH was 6-11, nitrate mainly reduced to N2 through co-action with acetate. Microbial community analysis revealed that as the initial pH increased from 4 to 11, the main hydrogen-producing microorganisms were gradually converted from Clostridium sensu stricto 12 sp. into Clostridium sensu stricto 1 sp, which leaded to changes in the hydrogen production process.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China.
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
| | - Yichuan Tan
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, PR China
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10
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Pratt M, Forbes JD, Knox NC, Van Domselaar G, Bernstein CN. Colorectal Cancer Screening in Inflammatory Bowel Diseases-Can Characterization of GI Microbiome Signatures Enhance Neoplasia Detection? Gastroenterology 2022; 162:1409-1423.e1. [PMID: 34998802 DOI: 10.1053/j.gastro.2021.12.287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/28/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
Current noninvasive methods for colorectal cancer (CRC) screening are not optimized for persons with inflammatory bowel diseases (IBDs), requiring patients to undergo frequent interval screening via colonoscopy. Although colonoscopy-based screening reduces CRC incidence in IBD patients, rates of interval CRC remain relatively high, highlighting the need for more targeted approaches. In recent years, the discovery of disease-specific microbiome signatures for both IBD and CRC has begun to emerge, suggesting that stool-based biomarker detection using metagenomics and other culture-independent technologies may be useful for personalized, early, noninvasive CRC screening in IBD patients. Here we discuss the utility of the stool microbiome as a noninvasive CRC screening tool. Comparing the performance of multiple microbiome-based CRC classifiers, including several multi-cohort meta-analyses, we find that noninvasive detection of colorectal adenomas and carcinomas from microbial biomarkers is an active area of study with promising early results.
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Affiliation(s)
- Molly Pratt
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jessica D Forbes
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Natalie C Knox
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Charles N Bernstein
- Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; University of Manitoba IBD Clinical and Research Centre, Winnipeg, Manitoba, Canada.
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. Nat Commun 2022; 13:586. [PMID: 35102136 PMCID: PMC8803835 DOI: 10.1038/s41467-022-28048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT. Here, Siranosian et al. provide evidence for rare transmission of commensal and pathogenic bacteria between the microbiomes of hospitalized adults, with important factors being roommate overlap and exposure to broad-spectrum antibiotics.
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Montoya ACV, da Silva Mazareli RC, Delforno TP, Centurion VB, de Oliveira VM, Silva EL, Varesche MBA. New Insights into Controlling Homoacetogenesis in the Co-digestion of Coffee Waste: Effect of Operational Conditions and Characterization of Microbial Communities. Appl Biochem Biotechnol 2021; 194:1458-1478. [PMID: 34739703 DOI: 10.1007/s12010-021-03725-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022]
Abstract
In this research batch reactors were operated with coffee processing waste and autochthonous microbial consortium, and a taxonomic and functional analysis was performed for phase I of stabilization of maximum H2 production and for phase II of maximum H2 consumption. During phase I, the reactor's operating conditions were pH 4.84 to 8.18, headspace 33.18% to 66.82%, and pulp and husk from 6.95 to 17.05 g/L. These assays continued for phase II, with initial pH conditions of 5.8-8.1, headspace of 33.18-66.82%, and pulp and husk remaining from phase I. The highest homoacetogenesis was observed in assay 5 with pH 7.7, 40% headspace, and 15 g/L of pulp and husk (initial concentrations of phase I). A relative abundance of Clostridium 41%, Lactobacillus 20% and Acetobacter 14% was observed in phase I. In phase II, there was a change in relative abundance of 21%, 63%, and 1%, respectively, and functional genes involved with autotrophic (formyltetrahydrofolate synthase) and heterotrophic (enolase) homoacetogenesis, butanol (3-hydroxybutyryl-CoA dehydrogenase), and propionic acid (propionate CoA-transferase) were identified. This study provides a new and amplified insight into the physicochemical and microbiological factors, which can be used to propose adequate operational conditions to maximize the bioenergy production and reduce homoacetogenesis in biological reactors.
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Affiliation(s)
- Alejandra Carolina Villa Montoya
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP, CEP 13563-120, Brazil.
| | - Raissa Cristina da Silva Mazareli
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP, CEP 13563-120, Brazil
| | | | - Victor Borin Centurion
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), State University of Campinas, Campinas, SP, CEP 13081-970, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), State University of Campinas, Campinas, SP, CEP 13081-970, Brazil
| | - Edson Luiz Silva
- Center of Exact Sciences and Technology, Department of Chemical Engineering, Federal University of São Carlos, São Carlos, SP, CEP 13565-905, Brazil
| | - Maria Bernadete Amâncio Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP, CEP 13563-120, Brazil.
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Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species. Virulence 2021; 12:1950-1964. [PMID: 34304696 PMCID: PMC8312603 DOI: 10.1080/21505594.2021.1950955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hungatella hathewayi has been observed to be a member of the gut microbiome. Unfortunately, little is known about this organism in spite of being associated with human fatalities; it is important to understand virulence mechanisms and epidemiological prospective to cause disease. In this study, a patient with chronic neurologic symptoms presented to the clinic with subsequent isolation of a strain with phenotypic characteristics suggestive of Clostridium difficile. However, whole-genome sequence found the organism to be H. hathewayi. Analysis including publicly available Hungatella genomes found substantial genomic differences as compared to the type strain, indicating this isolate was not C. difficile. We examined the whole-genome of Hungatella species and related genera, using comparative genomics to fully examine species identification and toxin production. Orthogonal phylogenetic using the 16S rRNA gene and entire genome analyses that included genome distance analyses using Genome-to-Genome Distance (GGDC), Average Nucleotide Identity (ANI), and a pan-genome analysis with inclusion of available public genomes determined the speciation to be Hungatella. Two clearly differentiated groups were identified, one including a reference H. hathewayi genome (strain DSM-13,479) and a second group that was determined to be H. effluvii, which included our clinical isolate. Also, some genomes reported as H. hathewayi were found to belong to other genera, including Clostridium and Faecalicatena. We show that the Hungatella species have an open pan-genome reflecting high genomic diversity. This study highlights the importance of correctly assigning taxonomic identification, particularly in disease-associated strains, to better understand virulence and therapeutic options.
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14
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Demir Çuha M, Er AG, Durukan BM, Karagöz A, Hazırolan G, Ünal S. A rare case of necrotizing fasciitis of the abdominal wall due to Hungatella effluvii and Streptococcus constellatus. Anaerobe 2021; 70:102409. [PMID: 34171472 DOI: 10.1016/j.anaerobe.2021.102409] [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: 03/09/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
We report a rare case of necrotizing fasciitis of the abdominal wall caused by Hungatella effluvii and Streptococcus constellatus. Necrotizing fasciitis has high mortality, so early diagnosis and aggressive treatment are essential for good clinical outcome. Identification of the microbial contribution to these infections is crucial for targeted antibiotic treatment.
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Affiliation(s)
- Mervenur Demir Çuha
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
| | - Ahmet Görkem Er
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Bekir Mert Durukan
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Alper Karagöz
- Department of Microbiology, Faculty of Molecular Biology and Genetics, Usak University, Usak, Turkey
| | - Gülşen Hazırolan
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Serhat Ünal
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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15
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Mishra A, Lai GC, Yao LJ, Aung TT, Shental N, Rotter-Maskowitz A, Shepherdson E, Singh GSN, Pai R, Shanti A, Wong RMM, Lee A, Khyriem C, Dutertre CA, Chakarov S, Srinivasan KG, Shadan NB, Zhang XM, Khalilnezhad S, Cottier F, Tan ASM, Low G, Chen P, Fan Y, Hor PX, Lee AKM, Choolani M, Vermijlen D, Sharma A, Fuks G, Straussman R, Pavelka N, Malleret B, McGovern N, Albani S, Chan JKY, Ginhoux F. Microbial exposure during early human development primes fetal immune cells. Cell 2021; 184:3394-3409.e20. [PMID: 34077752 PMCID: PMC8240556 DOI: 10.1016/j.cell.2021.04.039] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/09/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
The human fetal immune system begins to develop early during gestation; however, factors responsible for fetal immune-priming remain elusive. We explored potential exposure to microbial agents in utero and their contribution toward activation of memory T cells in fetal tissues. We profiled microbes across fetal organs using 16S rRNA gene sequencing and detected low but consistent microbial signal in fetal gut, skin, placenta, and lungs in the 2nd trimester of gestation. We identified several live bacterial strains including Staphylococcus and Lactobacillus in fetal tissues, which induced in vitro activation of memory T cells in fetal mesenteric lymph node, supporting the role of microbial exposure in fetal immune-priming. Finally, using SEM and RNA-ISH, we visualized discrete localization of bacteria-like structures and eubacterial-RNA within 14th weeks fetal gut lumen. These findings indicate selective presence of live microbes in fetal organs during the 2nd trimester of gestation and have broader implications toward the establishment of immune competency and priming before birth.
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Affiliation(s)
- Archita Mishra
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Ghee Chuan Lai
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Leong Jing Yao
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Thet Tun Aung
- Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Ra'anana 4353701, Israel
| | - Aviva Rotter-Maskowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Edwin Shepherdson
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Gurmit Singh Naranjan Singh
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Rhea Pai
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Adhika Shanti
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Regina Men Men Wong
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Andrea Lee
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Costerwell Khyriem
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Charles Antoine Dutertre
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Svetoslav Chakarov
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - K G Srinivasan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Xiao-Meng Zhang
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Shabnam Khalilnezhad
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Fabien Cottier
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Alrina Shin Min Tan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Gillian Low
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Phyllis Chen
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Yiping Fan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Pei Xiang Hor
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Avery Khoo May Lee
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228, Singpore
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Institute for Medical Immunology, ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Ankur Sharma
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore; Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia; Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Naomi McGovern
- Department of Pathology and Centre for Trophoblast Research, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore.
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; OBGYN-Academic Clinical Program, Duke-NUS, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore 119077, Singapore.
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China.
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16
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Bosák J, Lexa M, Fiedorová K, Gadara DC, Micenková L, Spacil Z, Litzman J, Freiberger T, Šmajs D. Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates. Front Immunol 2021; 12:671239. [PMID: 34054845 PMCID: PMC8163231 DOI: 10.3389/fimmu.2021.671239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022] Open
Abstract
Common variable immunodeficiency (CVID) is a clinically and genetically heterogeneous disorder with inadequate antibody responses and low levels of immunoglobulins including IgA that is involved in the maintenance of the intestinal homeostasis. In this study, we analyzed the taxonomical and functional metagenome of the fecal microbiota and stool metabolome in a cohort of six CVID patients without gastroenterological symptomatology and their healthy housemates. The fecal microbiome of CVID patients contained higher numbers of bacterial species and altered abundance of thirty-four species. Hungatella hathewayi was frequent in CVID microbiome and absent in controls. Moreover, the CVID metagenome was enriched for low-abundance genes likely encoding nonessential functions, such as bacterial motility and metabolism of aromatic compounds. Metabolomics revealed dysregulation in several metabolic pathways, mostly associated with decreased levels of adenosine in CVID patients. Identified features have been consistently associated with CVID diagnosis across the patients with various immunological characteristics, length of treatment, and age. Taken together, this initial study revealed expansion of bacterial diversity in the host immunodeficient conditions and suggested several bacterial species and metabolites, which have potential to be diagnostic and/or prognostic CVID markers in the future.
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Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Brno, Czechia
| | - Kristýna Fiedorová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czechia
- Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Darshak C. Gadara
- RECETOX Center, Faculty of Science, Masaryk University, Brno, Czechia
| | - Lenka Micenková
- RECETOX Center, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zdenek Spacil
- RECETOX Center, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Litzman
- Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czechia
- Department of Clinical Immunology and Allergology, St. Anne’s University Hospital in Brno, Brno, Czechia
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czechia
- Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
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17
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Brooks EF, Bhatt AS. The gut microbiome: a missing link in understanding the gastrointestinal manifestations of COVID-19? Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006031. [PMID: 33593727 PMCID: PMC8040733 DOI: 10.1101/mcs.a006031] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by infection with SARS-CoV-2, presents with a broad constellation of both respiratory and nonrespiratory symptoms, although it is primarily considered a respiratory disease. Gastrointestinal symptoms-including nausea, abdominal pain, vomiting, and diarrhea-rank chief among these. When coupled with the presence of viral RNA in fecal samples, the presence of gastrointestinal symptoms raises relevant questions regarding whether SARS-CoV-2 can productively infect the upper or lower gastrointestinal tract. Despite the well-documented prevalence of gastrointestinal symptoms and the high rate of SARS-CoV-2 fecal RNA shedding, the biological, clinical, and epidemiological relevance of these findings is unclear. Furthermore, the isolation of replication-competent virus from fecal samples has not been reproducibly and rigorously demonstrated. Although SARS-CoV-2 shedding likely occurs in a high proportion of patients, gastrointestinal symptoms affect only a subset of individuals. Herein, we summarize what is known about gastrointestinal symptoms and fecal viral shedding in COVID-19, explore the role of the gut microbiome in other respiratory diseases, speculate on the role of the gut microbiota in COVID-19, and discuss potential future directions. Taking these concepts together, we propose that studying gut microbiota perturbations in COVID-19 will enhance our understanding of the symptomology and pathophysiology of this novel devastating disease.
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Affiliation(s)
- Erin F Brooks
- Department of Medicine (Division of Hematology; Division of Blood and Marrow Transplantation), Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Ami S Bhatt
- Department of Medicine (Division of Hematology; Division of Blood and Marrow Transplantation), Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
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18
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Chan CWH, Leung TF, Choi KC, Tsui SKW, Wong CL, Chow KM, Chan JYW. Association of early-life gut microbiome and lifestyle factors in the development of eczema in Hong Kong infants. Exp Dermatol 2021; 30:859-864. [PMID: 33433023 DOI: 10.1111/exd.14280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/21/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022]
Abstract
Childhood eczema is common but its prevalence is variable in different regions of the world. In this study, we explore the associations of various risk factors such as the microbiome, environment, lifestyle, diet and maternal stress with the development of eczema among infants in Hong Kong. Upon enrolment in the study, the infants' parents provided demographic data by self-reporting. At enrolment and 1 year after birth, the infants' allergic conditions, lifestyles and dietary factors and the degree of maternal stress were assessed using various questionnaires. The infants' gut microbiomes were analysed by 16S RNA sequencing, and the longitudinal changes in various bacterial strains were compared between control and eczema-affected groups. Multivariate analyses (after adjustment for other significant factors) revealed that the changes in the abundance of Hungatella hathewayi in the gut were significantly associated with the development of eczema (p = 0.005). In conclusion, the increased abundance of Hungatella hathewayi was associated with an increased risk of developing eczema by 1 year of age. This study thus explored the potential risk factors for the development of eczema in Hong Kong infants, and sheds light on the possible association between early-life gut microbiome and other environmental factors.
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Affiliation(s)
- Carmen Wing Han Chan
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting Fan Leung
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kai Chow Choi
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - Cho Lee Wong
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ka Ming Chow
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Judy Yuet Wa Chan
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Shatin, Hong Kong
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19
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Hino S, Mizushima T, Kaneko K, Kawai E, Kondo T, Genda T, Yamada T, Hase K, Nishimura N, Morita T. Mucin-Derived O-Glycans Act as Endogenous Fiber and Sustain Mucosal Immune Homeostasis via Short-Chain Fatty Acid Production in Rat Cecum. J Nutr 2020; 150:2656-2665. [PMID: 32286621 DOI: 10.1093/jn/nxaa097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/27/2019] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Intestinal mucins escape digestion and enter the large bowel where they are degraded by the microbiota. To what extent and how mucins impact large-bowel physiology remain unclear. OBJECTIVE This study examined the large-bowel fermentation characteristics of mucins and mucin-derived O-glycan sugars and whether they affect gut immunity. METHODS Mucin secretion from the terminal ileum was determined from feces of ileorectostomized male Wistar rats (age 6 wk) fed an AIN76-based control diet (CD) for 15 d (experiment 1). Normal male Wistar rats (age 6 wk; 4 wk for experiment 4) were fed CD ± porcine stomach mucin (PM) at 6 or 12 g/kg diet, equivalent to 1.5 and 3 times the daily mucin secretion, for 14 d (experiment 2); CD ± N-acetylglucosamine (GlcNAc), fucose, or N-acetylneuraminic acid at 10 g/kg diet for 14 d (experiment 3); or CD ± PM (15 g/kg diet) or GlcNAc (10 g/kg diet) for 29 d (experiment 4). SCFAs, microbial composition, and cecal O-glycan content were assessed. IgA+ plasma cells and regulatory T cells and inflammatory cytokine expression in the cecum were evaluated (experiment 4). RESULTS Daily mucin secretion corresponded to 43.2 μmol of O-glycans. Cecal O-glycan contents were comparable between CD- and PM-fed rats. PM-fed rats harbored more mucin-degrading bacteria. Cecal concentrations of acetate (+37%) and n-butyrate (+73%) were higher in 12-g/kg PM diet-fed rats versus CD (P < 0.05). Among O-glycan sugars, only GlcNAc produced higher n-butyrate concentrations (+68%) versus CD (P < 0.05), with increased numbers of butyrate-producing bacteria. GlcNAc increased the abundance of IgA+ plasma cells (+29%) and regulatory T cells (+33%) versus CD, whereas PM increased IgA+ plasma cells (+25%) (all P < 0.05). GlcNAc and PM decreased expression of Tnfa (-30%, -40%) and Ifng (-30%, -70%) versus CD (all P < 0.05). CONCLUSIONS Mucin-derived O-glycans act as endogenous fiber and maintain mucosal immune homeostasis via large-bowel SCFA production in rats.
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Affiliation(s)
- Shingo Hino
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
| | - Takayasu Mizushima
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Katsunori Kaneko
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Erika Kawai
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Takashi Kondo
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Tomomi Genda
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Takahiro Yamada
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | - Naomichi Nishimura
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
| | - Tatsuya Morita
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
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20
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Sharing a β-Glucan Meal: Transcriptomic Eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi Consortium. Appl Environ Microbiol 2020; 86:AEM.01651-20. [PMID: 32801182 DOI: 10.1128/aem.01651-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022] Open
Abstract
Whole-transcriptome analysis was used to investigate the molecular interplay between three bacterial species that are members of the human gut microbiota. Bacteroides ovatus, Subdoligranulum variabile, and Hungatella hathewayi formed associations in cocultures fed barley β-glucan, a constituent of dietary fiber. B. ovatus depolymerized β-glucan and released, but did not utilize, 3-O-β-cellobiosyl-d-glucose (DP3) and 3-O-β-cellotriosyl-d-glucose (DP4). These oligosaccharides provided growth substrates for S. variabile and H. hathewayi with a preference for DP4 in the case of the latter species. There was increased transcription of a B. ovatus mixed-linkage-β-glucan utilization locus, as well as carbohydrate transporters in S. variabile and H. hathewayi when in batch coculture. Increased transcription of the β-glucan utilization locus did not occur in continuous culture. Evidence for interactions relating to provision of cobalamin, alterations to signaling, and modulation of the "stringent response" (an adaptation to nutrient deprivation) were detected. Overall, we established a bacterial consortium based on barley β-glucan in vitro, which can be used to investigate aspects of the functional blueprint of the human gut microbiota.IMPORTANCE The microbial community, mostly composed of bacterial species, residing in the human gut degrades and ferments polysaccharides derived from plants (dietary fiber) that would not otherwise be digested. In this way, the collective metabolic actions of community members extract additional energy from the human diet. While the variety of bacteria present in the microbial community is well known, the formation of bacterial consortia, and the consequent interactions that result in the digestion of dietary polysaccharides, has not been studied extensively. The importance of our work was the establishment, under laboratory conditions, of a consortium of gut bacteria that formed around a dietary constituent commonly present in cereals. This enabled the metabolic interplay between the bacterial species to be studied. This kind of knowledge is required to construct an interactive, metabolic blueprint of the microbial community that inhabits the human gut.
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Tall M, Lo C, Yimagou EK, Ndongo S, Pham T, Raoult D, Fournier PE, Fenollar F, Levasseur A. Description of Clostridium cagae sp. nov., Clostridium rectalis sp. nov. and Hathewaya massiliensis sp. nov., new anaerobic bacteria isolated from human stool samples. New Microbes New Infect 2020; 37:100719. [PMID: 32944255 PMCID: PMC7481820 DOI: 10.1016/j.nmni.2020.100719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022] Open
Abstract
Using culturomics methods, three strains were isolated, identified and characterized following the taxonogenomics concept. Clostridium cagae strain Marseille-P4344T (=CSURP4344), Clostridium rectalis strain Marseille-P4200T (=CSURP4200) and Hathewaya massiliensis strain Marseille-P3545T (=CSURP3545) were isolated from human stool samples. The phylogenetic reconstruction, phenotypic criteria and genomic analyses were carried out and demonstrated that these three bacteria are different from previously known bacterial species with standing in nomenclature and were classified as new members of the Clostridiaceae family.
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Affiliation(s)
- M.L. Tall
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E. Kuete Yimagou
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - T.P.T. Pham
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Levasseur
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
- Institut Universitaire de France (IUF), Paris, France
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Wei H, Li X, Tang L, Yao H, Ren Z, Wang C, Mu C, Shi C, Wang H. 16S rRNA gene sequencing reveals the relationship between gut microbiota and ovarian development in the swimming crab Portunus trituberculatus. CHEMOSPHERE 2020; 254:126891. [PMID: 32957291 DOI: 10.1016/j.chemosphere.2020.126891] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Gut microbiota executes many beneficial functions. In this study, the relationship between gut microbiota and ovarian development in the swimming crab P. trituberculatus was explored for the first time. A total of 28 phyla and 422 genera were identified across all samples. However, 105 differential operational taxonomic units, and four differential phyla (Gemmatimonadetes, Actinobacteria, Firmicutes, Marinimicrobia_(SAR406_clade)) were identified. At the genus level, 42 differential genera were identified and 144 bacterial indicators were identified. A key finding was that the relative abundance of 139 indicator bacteria detected in the anisomycin-2 mg/kg group (AK group) was higher than that of blank group (BK group), control group (CK group), SP600125-15 mg/kg group (SK group). In addition, the relative abundance of three indicator bacteria (OTU_236, OTU_1395, OTU_552) detected in the SK group was higher than that of the BK, CK and AK groups. It was also found that the relative abundance of 20 differential genera (Methyloversatilis, Coprococcus_1, Erysipelotrichaceae_UCG_003, Rikenella, Corynebacterium, Ruminiclostridium, Fusicatenibacter, [Eubacterium]_ruminantium_group, Rikenellaceae_RC9_gut_group, Bifidobacterium, Lachnospiraceae_NK4A136_group, Ruminococcaceae_UCG_014, Christensenellaceae_R_7_group, uncultured_Bacteroidales_bacterium, Coprococcus_2, Desulfovibrio, Aggregatibacter, Ambiguous_taxa, Alloprevotella and Ruminococcaceae_NK4A214_group) in the SK, BK, CK, and AK group samples were increasing. These differential genera may reveal the relationship between gut microbial communities and ovarian development in P. trituberculatus after injection with the JNK pathway inhibitor SP600125 or the activator anisomycin. In summary, this study provides a new understanding into the relationship between gut microbiota and ovarian development in response to stimulation with inhibitor or activator.
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Affiliation(s)
- Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Xing Li
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Hongzhi Yao
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Zhiming Ren
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Ce Shi
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
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Choksket S, Jain A, Sharma D, Grover V, Korpole S. Paraclostridium dentum, a novel species with pathogenic features isolated from human dental plaque sample. Anaerobe 2020; 65:102239. [PMID: 32758667 DOI: 10.1016/j.anaerobe.2020.102239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]
Abstract
A strictly anaerobic bacterial strain designated as SKVG24 was isolated from subgingival dental plaque samples of patients suffering from periodontitis. Cells were stained Gram-positive, rod shaped with endospore. The strain showed negative reaction to catalase and oxidase enzymes, but positive for gelatinase activity. Optimal growth was observed at 37 °C temperature and 7.0 pH. The 16S rRNA gene sequence BLAST analysis assigned strain SKVG24 to the genus Paraclostridium as it displayed 99.93% identity with P. benzoelyticum JC272T followed by P. bifermentans ATCC 638T (99.79%). However, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of the whole genome sequence showed <97% and <70% identity, respectively, with type strains of all closely related species. The G + C content of the DNA was 28.7 mol%. Total lipids profile showed presence of glycolipids as major lipids. Pathogenic features like hemolysis, gelatin hydrolysis and production of volatile sulfur compounds exhibited by strain SKVG24T were analogous to those observed in the established oral pathogenic strains. Further, whole genome sequence analysis confirmed the presence of genes encoding virulence factors and provided genomic insights on adaptation of the strain in oral environment. Based on the phenotypic and genetic differences with phylogenetic relatives, strain SKVG24T is proposed to represent a new species of the genus Paraclostridium with potential pathogenic ability, for which the name Paraclostridium dentum sp. nov., is suggested. The proposed type strain is SKVG24T (MTCC 12836T; = JCM 32760T).
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Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Ashish Jain
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
| | - Deepika Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Vishakha Grover
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India.
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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Wang Z, Jiang Y, Wang S, Zhang Y, Hu Y, Hu ZH, Wu G, Zhan X. Impact of total solids content on anaerobic co-digestion of pig manure and food waste: Insights into shifting of the methanogenic pathway. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 114:96-106. [PMID: 32659692 DOI: 10.1016/j.wasman.2020.06.048] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/26/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Dry anaerobic digestion (AD) has advantages over wet AD in treating high-solid organic wastes like livestock and food wastes, but an elevated total solids (TS) content would affect the AD performances. In this study, methane production of digesters co-digesting pig manure (PM) and food waste (FW) at different TS contents (R1, TS 5%; R2, TS 10%; R3, TS 15%; and R4, TS 20%) was assessed. The results showed the specific methane yield had no significant difference with the increase of TS contents from 5% to 15% (278.8-291.7 NmL/g VSadded), while it was reduced at a 20% TS content (259.8 NmL/g VSadded). Two peaks of total volatile fatty acids and daily methane production were observed in the high-solid digesters (R2-R4), while only one peak occurred in wet AD (R1). A new kinetics model was developed to describe the two-peak methane production behavior at high TS contents. The analysis on the microbial community structure clearly showed the different evolutions of methanogenic pathways in low and high solids content systems. In dry AD (R4), there was a general shifting from the acetoclastic pathway, to mixotrophic pathway and hydrogenotrophic pathway, with the dominance of mixotrophic and hydrogenotrophic methanogens.
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Affiliation(s)
- Zhongzhong Wang
- Civil Engineering, College of Engineering & Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland; MaREI Center for Marine and Renewable Energy, National University of Ireland, Galway, Ireland
| | - Yan Jiang
- Civil Engineering, College of Engineering & Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland; MaREI Center for Marine and Renewable Energy, National University of Ireland, Galway, Ireland
| | - Shun Wang
- Civil Engineering, College of Engineering & Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland; MaREI Center for Marine and Renewable Energy, National University of Ireland, Galway, Ireland
| | - Yizhen Zhang
- Civil Engineering, College of Engineering & Informatics, National University of Ireland, Galway, Ireland; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, China
| | - Yuansheng Hu
- Civil Engineering, College of Engineering & Informatics, National University of Ireland, Galway, Ireland
| | - Zhen-Hu Hu
- Department of Municipal Engineering, College of Civil Engineering, Hefei University of Technology, Hefei 230009, China
| | - Guangxue Wu
- Institute of Environmental Engineering and Management, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Xinmin Zhan
- Civil Engineering, College of Engineering & Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland; MaREI Center for Marine and Renewable Energy, National University of Ireland, Galway, Ireland.
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25
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Xia X, Wu WKK, Wong SH, Liu D, Kwong TNY, Nakatsu G, Yan PS, Chuang YM, Chan MWY, Coker OO, Chen Z, Yeoh YK, Zhao L, Wang X, Cheng WY, Chan MTV, Chan PKS, Sung JJY, Wang MH, Yu J. Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer. MICROBIOME 2020; 8:108. [PMID: 32678024 PMCID: PMC7367367 DOI: 10.1186/s40168-020-00847-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Altered microbiome composition and aberrant promoter hypermethylation of tumor suppressor genes (TSGs) are two important hallmarks of colorectal cancer (CRC). Here we performed concurrent 16S rRNA gene sequencing and methyl-CpG binding domain-based capture sequencing in 33 tissue biopsies (5 normal colonic mucosa tissues, 4 pairs of adenoma and adenoma-adjacent tissues, and 10 pairs of CRC and CRC-adjacent tissues) to identify significant associations between TSG promoter hypermethylation and CRC-associated bacteria, followed by functional validation of the methylation-associated bacteria. RESULTS Fusobacterium nucleatum and Hungatella hathewayi were identified as the top two methylation-regulating bacteria. Targeted analysis on bona fide TSGs revealed that H. hathewayi and Streptococcus spp. significantly correlated with CDX2 and MLH1 promoter hypermethylation, respectively. Mechanistic validation with cell-line and animal models revealed that F. nucleatum and H. hathewayi upregulated DNA methyltransferase. H. hathewayi inoculation also promoted colonic epithelial cell proliferation in germ-free and conventional mice. CONCLUSION Our integrative analysis revealed previously unknown epigenetic regulation of TSGs in host cells through inducing DNA methyltransferase by F. nucleatum and H. hathewayi, and established the latter as CRC-promoting bacteria. Video abstract.
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Affiliation(s)
- Xiaoxuan Xia
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - William Ka Kei Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Sunny Hei Wong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Dabin Liu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Thomas Ngai Yeung Kwong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Geicho Nakatsu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Pearlly S Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Yu-Ming Chuang
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan, Republic of China
| | - Michael Wing-Yan Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan, Republic of China
| | - Olabisi Oluwabukola Coker
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Liuyang Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Xiansong Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Wing Yin Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Matthew Tak Vai Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Paul Kay Sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Joseph Jao Yiu Sung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Maggie Haitian Wang
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
| | - Jun Yu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
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Li H, Xu H, Li Y, Jiang Y, Hu Y, Liu T, Tian X, Zhao X, Zhu Y, Wang S, Zhang C, Ge J, Wang X, Wen H, Bai C, Sun Y, Song L, Zhang Y, Hui R, Cai J, Chen J. Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms. Nat Commun 2020; 11:3218. [PMID: 32587239 PMCID: PMC7316982 DOI: 10.1038/s41467-020-16990-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
Unruptured intracranial aneurysm (UIA) is a life-threatening cerebrovascular condition. Whether changes in gut microbial composition participate in the development of UIAs remains largely unknown. We perform a case-control metagenome-wide association study in two cohorts of Chinese UIA patients and control individuals and mice that receive fecal transplants from human donors. After fecal transplantation, the UIA microbiota is sufficient to induce UIAs in mice. We identify UIA-associated gut microbial species link to changes in circulating taurine. Specifically, the abundance of Hungatella hathewayi is markedly decreased and positively correlated with the circulating taurine concentration in both humans and mice. Consistently, gavage with H. hathewayi normalizes the taurine levels in serum and protects mice against the formation and rupture of intracranial aneurysms. Taurine supplementation also reverses the progression of intracranial aneurysms. Our findings provide insights into a potential role of H. hathewayi-associated taurine depletion as a key factor in the pathogenesis of UIAs. Unruptured intracranial aneurysm (UIA) is a life-threatening cerebrovascular condition. Here the authors report altered gut microbiota including low abundance of Hungatella hathewayi in patients with UIAs, and show that supplementation with Hungatella hathewayi or the metabolite taurine prevents UIAs in mice.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Haochen Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Youxiang Li
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Yuhua Jiang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Yamin Hu
- Department of Cardiology, Cangzhou Central Hospital, Cangzhou, 061000, China
| | - Tingting Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Xueqing Tian
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Xihai Zhao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yandong Zhu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shuxia Wang
- Chinese PLA General Hospital and Chinese PLA Medical College, Beijing, 100853, China
| | - Chunrui Zhang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Jing Ge
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Xuliang Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Hongyan Wen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Congxia Bai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Yingying Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Li Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Yinhui Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Jun Cai
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Disease of China, National Center for Cardiovascular Diseases of China, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Jingzhou Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
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A Hungatella effluvii isolate in blood culture of a patient with hematochezia. Anaerobe 2020; 63:102211. [DOI: 10.1016/j.anaerobe.2020.102211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 01/20/2023]
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Wang Y, Chen X, Yu Y, Liu Y, Zhang Q, Bai J. Association between Gut Microbiota and Infant's Temperament in the First Year of Life in a Chinese Birth Cohort. Microorganisms 2020; 8:microorganisms8050753. [PMID: 32429579 PMCID: PMC7285300 DOI: 10.3390/microorganisms8050753] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 01/03/2023] Open
Abstract
Infant temperament characteristics play a critical role in children’s developmental pathways and can predict adulthood psychopathology. The diversity and composition of the gut microbiota are associated with human temperament in both adults and young children. However, the relationship between the gut microbiota and temperament in 12-month-old infants is rarely studied; this developmental period is when temperament reaches a relatively stable stage. We used high-throughput sequencing methods to explore whether temperament characteristics were associated with gut microbiota diversity and composition. Infants’ fecal samples were collected at 12 months of age for the gut microbiota analysis. Based on the primary caregivers’ reports, infants’ temperaments were measured using the Infant Behavior Questionnaire-revised (IBQ-R). This study included 51 infants, including 20 boys and 31 girls, with a mean age of 12.25 months. Results showed that soothability was positively correlated with maternal education level (β = 0.29, p = 0.043, adjust p = 0.025) and the abundance of Bifidobacterium genera (β = 0.62, p = 0.004, adjust p = 0.002). Conversely, cuddliness was negatively correlated with the abundance of Hungatella genera. There was no significant difference in temperament based on gender. This study demonstrated that gut microbiota composition was associated with temperament in 12-month-old infants. These results point to the importance of gut microbiota balance. Future studies on the mechanisms behind the gut microbiota affecting temperament are warranted.
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Affiliation(s)
- Ying Wang
- School of Health Sciences, Wuhan University, Wuhan 430071, China; (Y.W.); (X.C.); (Y.Y.)
| | - Xiaoli Chen
- School of Health Sciences, Wuhan University, Wuhan 430071, China; (Y.W.); (X.C.); (Y.Y.)
| | - Yun Yu
- School of Health Sciences, Wuhan University, Wuhan 430071, China; (Y.W.); (X.C.); (Y.Y.)
| | - Yanqun Liu
- School of Health Sciences, Wuhan University, Wuhan 430071, China; (Y.W.); (X.C.); (Y.Y.)
- Correspondence: (Y.L.); (Q.Z.); Tel.: +86-027-68758591 (Q.Z.)
| | - Qing Zhang
- School of Health Sciences, Wuhan University, Wuhan 430071, China; (Y.W.); (X.C.); (Y.Y.)
- Correspondence: (Y.L.); (Q.Z.); Tel.: +86-027-68758591 (Q.Z.)
| | - Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA 30322, USA;
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Haas KN, Blanchard JL. Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa. Int J Syst Evol Microbiol 2020; 70:23-34. [DOI: 10.1099/ijsem.0.003698] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kelly N. Haas
- Department of Biology, California State University Sacramento, Sacramento, California, USA
- Department of Dermatology, University of California Davis Medical Center, Sacramento, California, USA
| | - Jeffrey L. Blanchard
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
- Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, USA
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Yu HY, Meade A, Liu SJ. Phylogeny of Clostridium spp. Based on Conservative Genes and Comparisons with Other Trees. Microbiology (Reading) 2019. [DOI: 10.1134/s002626171904012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Liu X, Zheng H, Lu R, Huang H, Zhu H, Yin C, Mo Y, Wu J, Liu X, Deng M, Li D, Cheng B, Wu F, Liang Y, Guo H, Song H, Su Z. Intervening Effects of Total Alkaloids of Corydalis saxicola Bunting on Rats With Antibiotic-Induced Gut Microbiota Dysbiosis Based on 16S rRNA Gene Sequencing and Untargeted Metabolomics Analyses. Front Microbiol 2019; 10:1151. [PMID: 31214133 PMCID: PMC6555270 DOI: 10.3389/fmicb.2019.01151] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota dysbiosis induced by antibiotics is strongly connected with health concerns. Studying the mechanisms underlying antibiotic-induced gut microbiota dysbiosis could help to identify effective drugs and prevent many serious diseases. In this study, in rats with antibiotic-induced gut microbiota dysbiosis treated with total alkaloids of Corydalis saxicola Bunting (TACS), urinary and fecal biochemical changes and cecum microbial diversity were investigated using 16S rRNA gene sequencing analysis and untargeted metabolomics. The microbial diversity results showed that 10 genera were disturbed by the antibiotic treatment, and two of them were obviously restored by TACS. The untargeted metabolomics analysis identified 34 potential biomarkers in urine and feces that may be the metabolites that are most related to the mechanisms underlying antibiotic-induced gut microbiota dysbiosis and the therapeutic effects of TACS treatment. The biomarkers were involved in six metabolic pathways, comprising pathways related to branched-chain amino acid (BCAA), bile acid, arginine and proline, purine, aromatic amino acid, and amino sugar and nucleotide sugar metabolism. Notably, there was a strong correlation between these metabolic pathways and two gut microbiota genera (g__Blautia and g__Intestinibacter). The correlation analysis suggested that TACS might synergistically affect four of these metabolic pathways (BCAA, bile acid, arginine and proline, and purine metabolism), thereby modulating gut microbiota dysbiosis. Furthermore, we performed a molecular docking analysis involving simulating high-precision docking and using molecular pathway maps to illuminate the way that ligands (the five main alkaloid components of TACS) act on a complex molecular network, using CYP27A1 (a key enzyme in the bile acid synthesis pathway) as the target protein. This study provides a comprehensive overview of the intervening effects of TACS on the host metabolic phenotype and gut microbiome in rats with gut microbiota dysbiosis, and it presents new insights for the discovery of effective drugs and the best therapeutic approaches.
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Affiliation(s)
- Xi Liu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hua Zheng
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Rigang Lu
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Huimin Huang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hongjia Zhu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Chunli Yin
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yiyi Mo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Jinxia Wu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Xuwen Liu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Ming Deng
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Danfeng Li
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Bang Cheng
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Fang Wu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Yonghong Liang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hongwei Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hui Song
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Zhiheng Su
- Pharmaceutical College, Guangxi Medical University, Nanning, China
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El Hage R, Hernandez-Sanabria E, Calatayud Arroyo M, Props R, Van de Wiele T. Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem. Front Microbiol 2019; 10:1206. [PMID: 31214145 PMCID: PMC6554338 DOI: 10.3389/fmicb.2019.01206] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Metabolic syndrome is a growing public health concern. Efforts at searching for links with the gut microbiome have revealed that propionate is a major fermentation product in the gut with several health benefits toward energy homeostasis. For instance, propionate stimulates satiety-inducing hormones, leading to lower energy intake and reducing weight gain and associated risk factors. In (disease) scenarios where microbial dysbiosis is apparent, gut microbial production of propionate may be decreased. Here, we investigated the effect of a propionogenic bacterial consortium composed of Lactobacillusplantarum, Bacteroidesthetaiotaomicron, Ruminococcusobeum, Coprococcuscatus, Bacteroidesvulgatus, Akkermansiamuciniphila, and Veillonellaparvula for its potential to restore in vitro propionate concentrations upon antibiotic-induced microbial dysbiosis. Using the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME), we challenged the simulated colon microbiome with clindamycin. Addition of the propionogenic consortium resulted in successful colonization and subsequent restoration of propionate levels, while a positive effect on the mitochondrial membrane potential (ΔΨm) was observed in comparison with the controls. Our results support the development and application of next generation probiotics, which are composed of multiple bacterial strains with diverse functionality and phylogenetic background.
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Affiliation(s)
- Racha El Hage
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | | | | | - Ruben Props
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
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Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing. PLoS One 2019; 14:e0214085. [PMID: 30889205 PMCID: PMC6424423 DOI: 10.1371/journal.pone.0214085] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background Fecal microbiota transplantation (FMT) is an effective therapeutic approach for the treatment of functional gastrointestinal disease by restoring gut microbiota; however, there is a lack of sufficient understanding regarding which microbial populations successfully colonize the recipient gut. This study characterized microbial composition and diversity in patients diagnosed with chronic constipation at 1 month and 1 year after FMT. Methods We explored the microbial diversity of pre- and posttransplant stool specimens from patients using 16S rRNA gene sequencing, followed by functional analysis. Results The results identified 22 species of microorganisms colonized in the recipients from the donors at 1 month after FMT. One-year follow-up of the patient identified the colonization of 18 species of microorganisms, resulting in identification of species in significant abundance, including Bacteroides fragilis and Hungatella hathewayi in the recipient at 1 month after FMT and Dialister succinatiphilus, Coprococcus catus, and Sutterella stercoricanis at 1 year after FMT. The majority of the colonized species belong to the phylum Firmicutes and carry genes related to polysaccharide metabolism and that enhance the energy-harvesting efficiency of the host. Conclusion These results suggest that FMT is effective for the treatment of chronic constipation through the restoration and colonization of donor microbiota in the recipient gut up to 1 year after FMT.
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Clostridium indicum sp. nov., a novel anaerobic bacterium isolated from the sludge of an industrial effluent. Int J Syst Evol Microbiol 2019; 69:672-678. [DOI: 10.1099/ijsem.0.003199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Ezekiel CN, Ayeni KI, Ezeokoli OT, Sulyok M, van Wyk DAB, Oyedele OA, Akinyemi OM, Chibuzor-Onyema IE, Adeleke RA, Nwangburuka CC, Hajšlová J, Elliott CT, Krska R. High-Throughput Sequence Analyses of Bacterial Communities and Multi-Mycotoxin Profiling During Processing of Different Formulations of Kunu, a Traditional Fermented Beverage. Front Microbiol 2019; 9:3282. [PMID: 30687270 PMCID: PMC6333642 DOI: 10.3389/fmicb.2018.03282] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/17/2018] [Indexed: 02/05/2023] Open
Abstract
Kunu is a traditional fermented single or mixed cereals-based beverage popularly consumed in many parts of West Africa. Presently, the bacterial community and mycotoxin contamination profiles during processing of various kunu formulations have never been comprehensively studied. This study, therefore, investigated the bacterial community and multi-mycotoxin dynamics during the processing of three kunu formulations using high-throughput sequence analysis of partial 16S rRNA gene (hypervariable V3-V4 region) and liquid chromatography tandem mass spectrometry (LC-MS/MS), respectively. A total of 2,303 operational taxonomic units (OTUs) were obtained across six processing stages in all three kunu formulations. Principal coordinate analysis biplots of the Bray-Curtis dissimilarity between bacterial communities revealed the combined influences of formulations and processing steps. Taxonomically, OTUs spanned 13 phyla and 486 genera. Firmicutes (phylum) dominated (relative abundance) most of the processing stages, while Proteobacteria dominated the rest of the stages. Lactobacillus (genus taxa level) dominated most processing stages and the final product (kunu) of two formulations, whereas Clostridium sensu stricto (cluster 1) dominated kunu of one formulation, constituting a novel observation. We further identified Acetobacter, Propionibacterium, Gluconacetobacter, and Gluconobacter previously not associated with kunu processing. Shared phylotypes between all communities were dominated by lactic acid bacteria including species of Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Other shared phylotypes included notable acetic acid bacteria and potential human enteric pathogens. Ten mycotoxins [3-Nitropropionic acid, aflatoxicol, aflatoxin B1 (AFB1), AFB2, AFM1, alternariol (AOH), alternariolmethylether (AME), beauvericin (BEAU), citrinin, and moniliformin] were quantified at varying concentrations in ingredients for kunu processing. Except for AOH, AME, and BEAU that were retained at minimal levels of < 2 μg/kg in the final product, most mycotoxins in the ingredients were not detectable after processing. In particular, mycotoxin levels were substantially reduced by fermentation, although simple dilution and sieving also contributed to mycotoxin reduction. This study reinforces the perception of kunu as a rich source of bacteria with beneficial attributes to consumer health, and provides in-depth understanding of the microbiology of kunu processing, as well as information on mycotoxin contamination and reduction during this process. These findings may aid the development of starter culture technology for safe and quality kunu production.
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Affiliation(s)
- Chibundu N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Nigeria
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Kolawole I. Ayeni
- Department of Microbiology, Babcock University, Ilishan Remo, Nigeria
| | - Obinna T. Ezeokoli
- Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council-Institute for Soil, Climate and Water, Pretoria, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Michael Sulyok
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Deidre A. B. van Wyk
- Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council-Institute for Soil, Climate and Water, Pretoria, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | | | | | | | - Rasheed A. Adeleke
- Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council-Institute for Soil, Climate and Water, Pretoria, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Cyril C. Nwangburuka
- Department of Agriculture and Industrial Technology, Babcock University, Ilishan Remo, Nigeria
| | - Jana Hajšlová
- University of Chemistry and Technology, Prague, Czechia
| | - Christopher T. Elliott
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Rudolf Krska
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
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Chi X, Li J, Wang X, Zhang Y, Leu SY, Wang Y. Bioaugmentation with Clostridium tyrobutyricum to improve butyric acid production through direct rice straw bioconversion. BIORESOURCE TECHNOLOGY 2018; 263:562-568. [PMID: 29778795 DOI: 10.1016/j.biortech.2018.04.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/28/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
One-pot bioconversion is an economically attractive biorefinery strategy to reduce enzyme consumption. Direct conversion of lignocellulosic biomass for butyric acid production is still challenging because of competition among microorganisms. In a consolidated hydrolysis/fermentation bioprocessing (CBP) the microbial structure may eventually prefer the production of caproic acid rather than butyric acid production. This paper presents a new bioaugmentation approach for high butyric acid production from rice straw. By dosing 0.03 g/L of Clostridium tyrobutyricum ATCC 25755 in the CBP, an increase of 226% higher butyric acid was yielded. The selectivity and concentration also increased to 60.7% and 18.05 g/L, respectively. DNA-sequencing confirmed the shift of bacterial community in the augmented CBP. Butyric acid producer was enriched in the bioaugmented bacterial community and the bacteria related to long chain acids production was degenerated. The findings may be useful in future research and process design to enhance productivity of desired bio-products.
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Affiliation(s)
- Xue Chi
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China.
| | - Xin Wang
- School of Resources and Environment, Northeast Agriculture University, 59 Mucai Road, Harbin 150001, China
| | - Yafei Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China.
| | - Ying Wang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
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Onchuru TO, Martinez AJ, Kaltenpoth M. The cotton stainer's gut microbiota suppresses infection of a cotransmitted trypanosomatid parasite. Mol Ecol 2018; 27:3408-3419. [PMID: 29972876 DOI: 10.1111/mec.14788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 12/20/2022]
Abstract
The evolutionary and ecological success of many insects is attributed to mutualistic partnerships with bacteria that confer hosts with novel traits including food digestion, nutrient supplementation, detoxification of harmful compounds and defence against natural enemies. Dysdercus fasciatus firebugs (Hemiptera: Pyrrhocoridae), commonly known as cotton stainers, possess a simple but distinctive gut bacterial community including B vitamin-supplementing Coriobacteriaceae symbionts. In addition, their guts are often infested with the intestinal trypanosomatid parasite Leptomonas pyrrhocoris (Kinetoplastida: Trypanosomatidae). In this study, using experimental bioassays and fluorescence in situ hybridization (FISH), we report on the protective role of the D. fasciatus gut bacteria against L. pyrrhocoris. We artificially infected 2nd instars of dysbiotic and symbiotic insects with a parasite culture and measured parasite titres, developmental time and survival rates. Our results show that L. pyrrhocoris infection increases developmental time and slightly modifies the quantitative composition of the gut microbiota. More importantly, we found significantly higher parasite titres and a tendency towards lower survival rates in parasite-infected dysbiotic insects compared to symbiotic controls, indicating that the gut bacteria successfully interfere with the establishment or proliferation of L. pyrrhocoris. The colonization of symbiotic bacteria on the peritrophic matrix along the gut wall, as revealed by FISH, likely acts as a barrier blocking parasite attachment or entry into the hemolymph. Our findings show that in addition to being nutritionally important, D. fasciatus' gut bacteria complement the host's immune system in preventing parasite invasions and that a stable gut microbial community is integral for the host's health.
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Affiliation(s)
- Thomas O Onchuru
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany
| | - Adam J Martinez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz, Germany
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Sagheddu V, Patrone V, Miragoli F, Morelli L. Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR. Front Nutr 2017; 4:29. [PMID: 28695121 PMCID: PMC5483434 DOI: 10.3389/fnut.2017.00029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/09/2017] [Indexed: 12/17/2022] Open
Abstract
Delivery mode (natural vs. cesarean) and feeding type (breast vs. formula feeding) are relevant factors for neonatal gut colonization. Biomolecular methods have shown that the ecological structure of infant microbiota is more complex than previously proposed, suggesting a relevant presence of unculturable bacteria. It has also been postulated that among unculturable bacteria, hydrogenotrophic populations might play a key role in infant health. Sulfate-reducing bacteria (SRB), acetogens, and methanogenic archaea use hydrogenotrophic pathways within the human colon. However, to date, few studies have reported detection of hydrogenotrophic microorganisms in newborns, possibly because of limitations on available group-specific, culture-independent quantification procedures. In the present work, we analyzed 16 fecal samples of healthy babies aged 1-6 months by means of quantitative PCR (qPCR) targeting the 16S rRNA or metabolic functional genes and by denaturing gradient gel electrophoresis (DGGE). qPCR data showed quantifiable levels of methanogens, SRB, and acetogens in all samples, indicating that the relative abundances of these microbial groups were not affected by delivery mode (natural vs. caesarian). DGGE revealed a high prevalence of the Blautia genus within the acetogenic bacteria despite strong interindividual variability. Our preliminary results suggest that hydrogenotrophic microorganisms, which have been a neglected group to date, should be included in future ecological and metabolic studies evaluating the infant intestinal microbiota.
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Affiliation(s)
- Valeria Sagheddu
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Vania Patrone
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesco Miragoli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Lorenzo Morelli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Khanna S, Button JE, Lombardo MJ, Vulic M, Henn MR, Cook DN, Pomerantz RJ, Hohmann EL. Reply to Lagier et al. J Infect Dis 2017; 215:162-164. [DOI: 10.1093/infdis/jiw490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 11/15/2022] Open
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Perz V, Hromic A, Baumschlager A, Steinkellner G, Pavkov-Keller T, Gruber K, Bleymaier K, Zitzenbacher S, Zankel A, Mayrhofer C, Sinkel C, Kueper U, Schlegel K, Ribitsch D, Guebitz GM. An Esterase from Anaerobic Clostridium hathewayi Can Hydrolyze Aliphatic-Aromatic Polyesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2899-907. [PMID: 26878094 DOI: 10.1021/acs.est.5b04346] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recently, a variety of biodegradable polymers have been developed as alternatives to recalcitrant materials. Although many studies on polyester biodegradability have focused on aerobic environments, there is much less known on biodegradation of polyesters in natural and artificial anaerobic habitats. Consequently, the potential of anaerobic biogas sludge to hydrolyze the synthetic compostable polyester PBAT (poly(butylene adipate-co-butylene terephthalate) was evaluated in this study. On the basis of reverse-phase high-performance liquid chromatography (RP-HPLC) analysis, accumulation of terephthalic acid (Ta) was observed in all anaerobic batches within the first 14 days. Thereafter, a decline of Ta was observed, which occurred presumably due to consumption by the microbial population. The esterase Chath_Est1 from the anaerobic risk 1 strain Clostridium hathewayi DSM-13479 was found to hydrolyze PBAT. Detailed characterization of this esterase including elucidation of the crystal structure was performed. The crystal structure indicates that Chath_Est1 belongs to the α/β-hydrolases family. This study gives a clear hint that also micro-organisms in anaerobic habitats can degrade manmade PBAT.
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Affiliation(s)
- Veronika Perz
- Austrian Centre of Industrial Biotechnology ACIB , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
| | - Altijana Hromic
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz , Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Armin Baumschlager
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz , Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Klaus Bleymaier
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Sabine Zitzenbacher
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Armin Zankel
- Institute of Electron Microscopy and Nanoanalysis, Graz University of Technology , Steyrergasse 17/III, 8010 Graz, Austria
| | - Claudia Mayrhofer
- Institute of Electron Microscopy and Nanoanalysis, Graz University of Technology , Steyrergasse 17/III, 8010 Graz, Austria
| | - Carsten Sinkel
- BASF SE , Carl-Bosch-Straße 38, 67056 Ludwigshafen, Germany
| | - Ulf Kueper
- BASF SE , Carl-Bosch-Straße 38, 67056 Ludwigshafen, Germany
| | | | - Doris Ribitsch
- Austrian Centre of Industrial Biotechnology ACIB , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology ACIB , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
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Dione N, Sankar S, Lagier JC, Khelaifia S, Michele C, Armstrong N, Richez M, Abrahão J, Raoult D, Fournier PE. Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 2016; 10:66-76. [PMID: 26937282 PMCID: PMC4753391 DOI: 10.1016/j.nmni.2016.01.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 01/09/2023] Open
Abstract
Anaerosalibacter massiliensis sp. nov. strain ND1(T) (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, the genome of which is described here, was isolated from the faecal flora of a 49-year-old healthy Brazilian man. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod and member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3 197 911 bp long genome (one chromosome but no plasmid) contains 3271 protein-coding and 62 RNA genes, including six rRNA genes.
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Affiliation(s)
- N. Dione
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S.A. Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - C. Michele
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - M. Richez
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
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Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 2016; 66:1009-1016. [DOI: 10.1099/ijsem.0.000824] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Fred A. Rainey
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
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Schaubeck M, Clavel T, Calasan J, Lagkouvardos I, Haange SB, Jehmlich N, Basic M, Dupont A, Hornef M, von Bergen M, Bleich A, Haller D. Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence. Gut 2016; 65:225-37. [PMID: 25887379 PMCID: PMC4752651 DOI: 10.1136/gutjnl-2015-309333] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/21/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Dysbiosis of the intestinal microbiota is associated with Crohn's disease (CD). Functional evidence for a causal role of bacteria in the development of chronic small intestinal inflammation is lacking. Similar to human pathology, TNF(deltaARE) mice develop a tumour necrosis factor (TNF)-driven CD-like transmural inflammation with predominant ileal involvement. DESIGN Heterozygous TNF(deltaARE) mice and wildtype (WT) littermates were housed under conventional (CONV), specific pathogen-free (SPF) and germ-free (GF) conditions. Microbial communities were analysed by high-throughput 16S ribosomal RNA gene sequencing. Metaproteomes were measured using LC-MS. Temporal and spatial resolution of disease development was followed after antibiotic treatment and transfer of microbial communities into GF mice. Granulocyte infiltration and Paneth cell function was assessed by immunofluorescence and gene expression analysis. RESULTS GF-TNF(deltaARE) mice were free of inflammation in the gut and antibiotic treatment of CONV-TNF(deltaARE) mice attenuated ileitis but not colitis, demonstrating that disease severity and location are microbiota-dependent. SPF-TNF(deltaARE) mice developed distinct ileitis-phenotypes associated with gradual loss of antimicrobial defence. 16S analysis and metaproteomics revealed specific compositional and functional alterations of bacterial communities in inflamed mice. Transplantation of disease-associated but not healthy microbiota transmitted CD-like ileitis to GF-TNF(deltaARE) recipients and triggered loss of lysozyme and cryptdin-2 expression. Monoassociation of GF-TNF(deltaARE) mice with the human CD-related Escherichia coli LF82 did not induce ileitis. CONCLUSIONS We provide clear experimental evidence for the causal role of gut bacterial dysbiosis in the development of chronic ileal inflammation with subsequent failure of Paneth cell function.
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Affiliation(s)
- Monika Schaubeck
- Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany
| | - Thomas Clavel
- ZIEL-Institute for Food and Health, Technische Universität München, Freising-Weihenstephan, Germany
| | - Jelena Calasan
- Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany
| | - Ilias Lagkouvardos
- ZIEL-Institute for Food and Health, Technische Universität München, Freising-Weihenstephan, Germany
| | - Sven Bastiaan Haange
- Department of Proteomics, Helmholtz-Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz-Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Marijana Basic
- Institut for Medical Microbiology, RWTH University, Aachen, Germany
| | - Aline Dupont
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany,Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Mathias Hornef
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany,Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz-Centre for Environmental Research—UFZ, Leipzig, Germany,UFZ, Department of Metabolomics, Helmholtz-Centre for Environmental Research, Leipzig, Germany,Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Aalborg, Denmark
| | - André Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany,ZIEL-Institute for Food and Health, Technische Universität München, Freising-Weihenstephan, Germany
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Randazzo A, Kornreich A, Lissoir B. A Clostridium hathewayi isolate in blood culture of a patient with an acute appendicitis. Anaerobe 2015; 35:44-7. [PMID: 26187681 DOI: 10.1016/j.anaerobe.2015.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/01/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Clostridium species is a group of anaerobic bacteria constituting the colonic microflora of the intestinal tract. Since molecular methodologies based on 16 rRNA have been established for the classification and the recognition of bacterial species, more than 150 species of Clostridium have been described. Most are considered harmless saprophytes; however, these bacteria may be involved in a wide variety of infections and may be a common cause of enteritis and enterotoxemias in humans. CASE PRESENTATION We present the case of a 60-year-old Asian patient admitted in the emergency room with an acute appendicitis where a blood culture showed the presence of a Clostridium hathewayi. This microorganism is an anaerobic bacteria described in 2001 as a Gram negative end-pointed bacillus, usually endospore-forming. It was reclassified in 2014 as Hungatella hathewayi. A literature review has been performed to find articles relating to this bacteria in a clinical case. CONCLUSION C. hathewayi is microorganism recently reclassified as Hungatella hathewayi. Its growth in blood cultures has been reported in a few cases in the literature. Although only a few articles have reported its involvement in clinical infections, we assess that its part in the cause of the illness should be evaluated.
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Affiliation(s)
- Adrien Randazzo
- Medical Laboratory, Grand Hôpital de Charleroi, Rue Marguerite Depasse 6, 6060 Gilly, Belgium.
| | - Anne Kornreich
- Medical Laboratory, Grand Hôpital de Charleroi, Rue Marguerite Depasse 6, 6060 Gilly, Belgium.
| | - Bénédicte Lissoir
- Department of Microbiology, Medical Laboratory, Grand Hôpital de Charleroi, Rue Marguerite Depasse 6, 6060 Gilly, Belgium.
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Identification of a two-component signal transduction system that regulates maltose genes in Clostridium perfringens. Anaerobe 2014; 30:199-204. [DOI: 10.1016/j.anaerobe.2014.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 11/23/2022]
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