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Rizzello F, Viciani E, Gionchetti P, Filippone E, Imbesi V, Melotti L, Dussias NK, Salice M, Santacroce B, Padella A, Velichevskaya A, Marcante A, Castagnetti A. Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients. Front Cell Infect Microbiol 2024; 14:1352202. [PMID: 38510960 PMCID: PMC10952111 DOI: 10.3389/fcimb.2024.1352202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. Methods In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. Results We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as Enterococcus, Streptococcus, and Actinomyces. Of note, the Candida genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that Saccharomycetales unassigned fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus Bilophila in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. Conclusions COVID-19 was associated with opportunistic bacterial pathogens, and Candida was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.
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Affiliation(s)
- Fernando Rizzello
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | | | - Paolo Gionchetti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Eleonora Filippone
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Veronica Imbesi
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
| | - Laura Melotti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Nikolas Konstantine Dussias
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Marco Salice
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
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DeSana AJ, Estus S, Barrett TA, Saatman KE. Acute gastrointestinal permeability after traumatic brain injury in mice precedes a bloom in Akkermansia muciniphila supported by intestinal hypoxia. Sci Rep 2024; 14:2990. [PMID: 38316862 PMCID: PMC10844296 DOI: 10.1038/s41598-024-53430-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Traumatic brain injury (TBI) increases gastrointestinal morbidity and associated mortality. Clinical and preclinical studies implicate gut dysbiosis as a consequence of TBI and an amplifier of brain damage. However, little is known about the association of gut dysbiosis with structural and functional changes of the gastrointestinal tract after an isolated TBI. To assess gastrointestinal dysfunction, mice received a controlled cortical impact or sham brain injury and intestinal permeability was assessed at 4 h, 8 h, 1 d, and 3 d after injury by oral administration of 4 kDa FITC Dextran prior to euthanasia. Quantification of serum fluorescence revealed an acute, short-lived increase in permeability 4 h after TBI. Despite transient intestinal dysfunction, no overt morphological changes were evident in the ileum or colon across timepoints from 4 h to 4 wks post-injury. To elucidate the timeline of microbiome changes after TBI, 16 s gene sequencing was performed on DNA extracted from fecal samples collected prior to and over the first month after TBI. Differential abundance analysis revealed that the phylum Verrucomicrobiota was increased at 1, 2, and 3 d after TBI. The Verrucomicrobiota species was identified by qPCR as Akkermansia muciniphila, an obligate anaerobe that resides in the intestinal mucus bilayer and produces short chain fatty acids (e.g. butyrate) utilized by intestinal epithelial cells. We postulated that TBI promotes intestinal changes favorable for the bloom of A. muciniphila. Consistent with this premise, the relative area of mucus-producing goblet cells in the medial colon was significantly increased at 1 d after injury, while colon hypoxia was significantly increased at 3 d. Our findings reveal acute gastrointestinal functional changes coupled with an increase of beneficial bacteria suggesting a potential compensatory response to systemic stress after TBI.
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Affiliation(s)
- Anthony J DeSana
- Department of Physiology, University of Kentucky, Biomedical and Biological Sciences Research Building (BBSRB), B473, 741 South Limestone St., Lexington, KY, 40536, USA
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Biomedical and Biological Sciences Research Building (BBSRB), B473, 741 South Limestone St., Lexington, KY, 40536, USA
| | - Steven Estus
- Department of Physiology, University of Kentucky, Biomedical and Biological Sciences Research Building (BBSRB), B473, 741 South Limestone St., Lexington, KY, 40536, USA
- Sanders Brown Center on Aging, University of Kentucky, Lee T. Todd, Jr. Building, Rm: 537, 789 South Limestone St., Lexington, KY, 40536, USA
| | - Terrence A Barrett
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine - Digestive Health, University of Kentucky, Lexington, KY, 40536, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Medical Science Building, MN649, 780 Rose St., Lexington, KY, 40536, USA
| | - Kathryn E Saatman
- Department of Physiology, University of Kentucky, Biomedical and Biological Sciences Research Building (BBSRB), B473, 741 South Limestone St., Lexington, KY, 40536, USA.
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Biomedical and Biological Sciences Research Building (BBSRB), B473, 741 South Limestone St., Lexington, KY, 40536, USA.
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Vidmar Šimic M, Maver A, Zimani AN, Hočevar K, Peterlin B, Kovanda A, Premru-Sršen T. Oral microbiome and preterm birth. Front Med (Lausanne) 2023; 10:1177990. [PMID: 37608830 PMCID: PMC10441245 DOI: 10.3389/fmed.2023.1177990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Background The etiology of preterm birth (PTB) is heterogeneous and not yet well known. Maternal periodontal disease has been investigated for decades and is a known risk factor for adverse pregnancy outcomes. However, no particular bacterial species or higher taxonomic order has been found as causative of PTB, leading to studies of the whole oral microbiome. In order to determine if and how the composition of the oral microbiome is associated with PTB, we performed a large case-control study including women with term (TB) and PTB. Methods We compared oral microbiomes in PTB to TB, to examine differences in the microbial richness, diversity, and differential abundance of specific taxa. We obtained oral swab samples from 152 Caucasian pregnant women who were classified as either PTB (≤36 6/7 weeks, n = 61) or TB (≥38 0/7 weeks, n = 91) in exclusion of any other major medical or obstetric conditions. The oral microbiomes of these women were characterized by 16S ribosomal RNA (rRNA) gene sequencing of the V3-V4 region on the MiSeq platform. Results The dominant microorganisms at the phylum level in all pregnant women regardless of birth week outcomes as belonging to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. The phyla Firmicutes and Bacteroidetes were relatively more abundant in women with a PTB than in women with a TB, while Proteobacteria was less prevalent in women with a PTB. At the genus level, Veillonella, Prevotella, and Capnocytophaga were enriched in the PTB, and while many of the members of these genera could not be resolved to the species level, Veillonella massillensis was shown to be increased in the PTB group. Conclusion We identified the genera Veillonella, Prevotella, and Capnocytophaga in the maternal oral microbiome as being associated with PTB independently of clinically apparent infection, uterine anomalies, and other pregnancy complications, including placenta previa, and placental abruption. The clarification of the role of those taxa in the etiology of PTB merits further research.
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Affiliation(s)
- Marijana Vidmar Šimic
- Division of Obstetrics and Gynecology, Department of Perinatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Keli Hočevar
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Premru-Sršen
- Division of Obstetrics and Gynecology, Department of Perinatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Taladrid D, Zorraquín‐Peña I, Molinero N, Silva M, Manceñido N, Pajares R, Bartolomé B, Moreno‐Arribas MV. Polyphenols and Ulcerative Colitis: An Exploratory Study of the Effects of Red Wine Consumption on Gut and Oral Microbiome in Active-Phase Patients. Mol Nutr Food Res 2022; 66:e2101073. [PMID: 35633101 PMCID: PMC9787944 DOI: 10.1002/mnfr.202101073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/09/2022] [Indexed: 12/30/2022]
Abstract
SCOPE This paper explores the effects of moderate red wine consumption on the clinical status and symptomatology of patients with ulcerative colitis (UC), including the study of the oral and intestinal microbiome. METHODS AND RESULTS A case control intervention study in UC patients is designed. Intervention patients (n = 5) consume red wine (250 mL day-1 ) for 4 weeks whereas control patients (n = 5) do not. Moderate wine consumption significantly (p < 0.05) improves some clinical parameters related to serum iron, and alleviates intestinal symptoms as evaluated by the IBDQ-32 questionnaire. 16S rRNA gene sequencing indicate a non-significant (p > 0.05) increase in bacterial alpha diversity after wine intervention in both saliva and fecal microbiota. Additional comparison of taxonomic data between UC patients (n = 10) and healthy subjects (n = 8) confirm intestinal dysbiosis for the UC patients. Finally, analysis of fecal metabolites (i.e., phenolic acids and SCFAs) indicates a non-significant increase (p > 0.05) for the UC patients that consumed wine. CONCLUSIONS Moderate and regular red wine intake seems to improve the clinical status and symptoms of UC patients in the active phase of the disease. However, studies with a greater sample size are required to achieve conclusive results.
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Affiliation(s)
- Diego Taladrid
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Irene Zorraquín‐Peña
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Natalia Molinero
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Mariana Silva
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Noemi Manceñido
- Hospital Universitario “Infanta Sofia”, P.° de Europa34, 28703 San Sebastián de los ReyesMadridSpain
| | - Ramón Pajares
- Hospital Universitario “Infanta Sofia”, P.° de Europa34, 28703 San Sebastián de los ReyesMadridSpain
| | - Begoña Bartolomé
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
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Williamson BD, Hughes JP, Willis AD. A multiview model for relative and absolute microbial abundances. Biometrics 2022; 78:1181-1194. [PMID: 34048057 PMCID: PMC8982138 DOI: 10.1111/biom.13503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/30/2022]
Abstract
The absolute abundance of bacterial taxa in human host-associated environments plays a critical role in reproductive and gastrointestinal health. However, obtaining the absolute abundance of many bacterial species is typically prohibitively expensive. In contrast, relative abundance data for many species are comparatively cheap and easy to collect (e.g., with universal primers for the 16S rRNA gene). In this paper, we propose a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa. Our method provides point and interval estimates for the absolute abundance of all taxa. Crucially, our proposal accounts for differences in the efficiency of taxon detection in the relative and absolute abundance data. We show that modeling taxon-specific efficiencies substantially reduces the estimation error for absolute abundance, and controls the coverage of interval estimators. We demonstrate the performance of our proposed method via a simulation study, a study of the effect of HIV acquisition on microbial abundances, and a sensitivity study where we jackknife the taxa with observed absolute abundances.
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Affiliation(s)
| | - James P. Hughes
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Amy D. Willis
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
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Puntillo M, Peralta G, Bürgi M, Huber P, Gaggiotti M, Binetti A, Vinderola G. Metaprofiling of the bacterial community in sorghum silages inoculated with lactic acid bacteria. J Appl Microbiol 2022; 133:2375-2389. [PMID: 35778976 DOI: 10.1111/jam.15698] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/13/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022]
Abstract
AIMS to characterize the fermentation process and bacterial diversity of sorghum silage inoculated with Lactiplantibacillus plantarum LpAv, Pediococcus pentosaceus PpM and Lacticaseibacillus paracasei LcAv. METHODS AND RESULTS chopped sorghum was ensiled using the selected strains. Physicochemical parameters (Ammonia Nitrogen/Total Nitrogen, Dry Matter, Crude Protein, Acid Detergent Fiber, Neutral Detergent Fiber, Acid Detergent Lignin, Ether Extract and Ashes), bacterial counts, cell cytometry and 16sRNA sequencing were performed to characterize the ensiling process and an animal trial (BALB/c mice) was conducted in order to preliminary explore the potential of sorghum silage to promote animal gut health. After 30 days of ensiling, the genus Lactobacillus comprised 68.4 ± 2.3 % and 73.5 ± 1.8 % of relative abundance, in control and inoculated silages respectively. Richness (Chao1 index) in inoculated samples, but not in control silages, diminished along ensiling, suggesting the domination of fermentation by the inoculated LAB. A trend in conferring enhanced protection against Salmonella infection was observed in the mouse model used to explore the potential to promote gut health of sorghum silage. CONCLUSIONS the LAB strains used in this study were able to dominate sorghum fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY this is the first report using metaprofiling of 16sRNA to characterize sorghum silage, showing a microbiological insight where resident and inoculated LAB strains overwhelmed the epiphytic microbiota, inhibiting potential pathogens of the genus Klebsiella.
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Affiliation(s)
- Melisa Puntillo
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería. Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Guillermo Peralta
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería. Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Milagros Bürgi
- Centro Biotecnológico del Litoral, FBCB (CONICET-UNL), Santa Fe, Argentina
| | - Paula Huber
- Laboratorio de Plancton, Instituto Nacional de Limnología (INALI, UNL-CONICET), Universidad Nacional del Litoral, Santa Fe, Argentina, and Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos (SP), Brazil
| | - Mónica Gaggiotti
- Laboratorio de Calidad de Leche y Agroindustria, INTA EEA Rafaela, Santa Fe, Argentina
| | - Ana Binetti
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería. Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería. Química, Universidad Nacional del Litoral, Santa Fe, Argentina
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7
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FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities. Int J Food Microbiol 2022; 372:109696. [DOI: 10.1016/j.ijfoodmicro.2022.109696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/04/2023]
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Malinowska AM, Kok DE, Steegenga WT, Hooiveld GJEJ, Chmurzynska A. Human gut microbiota composition and its predicted functional properties in people with western and healthy dietary patterns. Eur J Nutr 2022; 61:3887-3903. [PMID: 35748920 PMCID: PMC9596542 DOI: 10.1007/s00394-022-02928-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Some dietary habits cluster together, and for this reason it is advised to study the impact of entire dietary patterns on human health, rather than that of individual dietary habits. The main objective of this study was to evaluate differences in gut microbiota composition and their predicted functional properties between people with a healthy (HDP) and western (WDP) dietary pattern. METHODS A cross-sectional, observational study was carried out on 200 participants enrolled 2017-2018 in Poznań, Poland, equally distributed into HDP and WDP groups. Diet was estimated using 3-day food records and information on stool transit times was collected. Fecal microbiota composition was assessed by 16S rRNA gene sequencing and its functional properties were predicted by the PICRUSt2 workflow. RESULTS The α-diversity did not differ between people with WDP and HDP, but β-diversity was associated with dietary pattern. People with HDP had higher relative abundances (RA) of Firmicutes and Faecalibacterium and lower RA of Bacteroidota and Escherichia-Shigella than participants with WDP. Only a small proportion of the variance in microbiota composition (1.8%) and its functional properties (2.9%) could be explained by dietary intake (legumes, simple sugars and their sources, like fruit, soft drinks) and stool transit characteristics. CONCLUSION Gut microbiota composition and predicted metabolic potential is shaped by overall diet quality as well as the frequency of defecation; however, the cumulative effect of these explain only a relatively low proportion of variance.
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Affiliation(s)
- Anna M Malinowska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624, Poznan, Poland.
- Division of Human Nutrition and Health, Wageningen University and Research, PO Box 17, 6700 AA, Wageningen, The Netherlands.
| | - Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University and Research, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Wilma T Steegenga
- Division of Human Nutrition and Health, Wageningen University and Research, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Guido J E J Hooiveld
- Division of Human Nutrition and Health, Wageningen University and Research, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Agata Chmurzynska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624, Poznan, Poland
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Geological activity shapes the microbiome in deep-subsurface aquifers by advection. Proc Natl Acad Sci U S A 2022; 119:e2113985119. [PMID: 35696589 PMCID: PMC9231496 DOI: 10.1073/pnas.2113985119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sheltered from radiation and asteroid strikes in Earth’s early history and home to a significant portion of today’s prokaryotic biomass, the deep subsurface could hold keys to understanding the early and continuing evolution of life. However, the processes that shape the distribution of subsurface microbial communities remain poorly understood due to sample inaccessibility. Here, at a deep-underground fractured hard-rock aquifer, we show that fracture activity leads to altered groundwater flow that drives profound changes in fluid-associated microbial communities by physical transport instead of environmental selection. We thereby identify advection induced by geological activity (a notable trigger for fracture activity) as a prominent yet overlooked mechanism shaping subsurface biogeography with potentially profound implications for life’s evolutionary history. Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.
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Modulation of Gut Microbiota and Neuroprotective Effect of a Yeast-Enriched Beer. Nutrients 2022; 14:nu14122380. [PMID: 35745108 PMCID: PMC9228237 DOI: 10.3390/nu14122380] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Beer is the most consumed alcoholic beverage worldwide. It is rich in nutrients, and with its microbial component it could play a role in gut microbiota modulation. Conflicting data are currently available regarding the consequences of alcohol and alcohol-containing beverages on dementia and age-associated disorders including Alzheimer’s disease (AD), a neurodegeneration characterized by protein aggregation, inflammatory processes and alterations of components of the gut–brain axis. The effects of an unfiltered and unpasteurized craft beer on AD molecular hallmarks, levels of gut hormones and composition of micro/mycobiota were dissected using 3xTg-AD mice. In addition, to better assess the role of yeasts, beer was enriched with the same Saccharomyces cerevisiae strain used for brewing. The treatment with the yeast-enriched beer ameliorated cognition and favored the reduction of Aβ(1-42) and pro-inflammatory molecules, also contributing to an increase in the concentration of anti-inflammatory cytokines. A significant improvement in the richness and presence of beneficial taxa in the gut bacterial population of the 3xTg-AD animals was observed. In addition, the fungal order, Sordariomycetes, associated with gut inflammatory conditions, noticeably decreased with beer treatments. These data demonstrate, for the first time, the beneficial effects of a yeast-enriched beer on AD signs, suggesting gut microbiota modulation as a mechanism of action.
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Lavelle A, Nancey S, Reimund JM, Laharie D, Marteau P, Treton X, Allez M, Roblin X, Malamut G, Oeuvray C, Rolhion N, Dray X, Rainteau D, Lamaziere A, Gauliard E, Kirchgesner J, Beaugerie L, Seksik P, Peyrin-Biroulet L, Sokol H. Fecal microbiota and bile acids in IBD patients undergoing screening for colorectal cancer. Gut Microbes 2022; 14:2078620. [PMID: 35638103 PMCID: PMC9176255 DOI: 10.1080/19490976.2022.2078620] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Due to the potential role of the gut microbiota and bile acids in the pathogenesis of both inflammatory bowel disease (IBD) and sporadic colorectal cancer, we aimed to determine whether these factors were associated with colorectal cancer in IBD patients. 215 IBD patients and 51 non-IBD control subjects were enrolled from 10 French IBD centers between September 2011 and July 2018. Fecal samples were processed for bacterial 16S rRNA gene sequencing and bile acid profiling. Demographic, clinical, endoscopic, and histological outcomes were recorded. Characteristics of IBD patients included: median age: 41.6 (IQR 22); disease duration 13.2 (13.1); 47% female; 21.9% primary sclerosing cholangitis; 109 patients with Crohn's disease (CD); 106 patients with ulcerative colitis (UC). The prevalence of cancer was 2.8% (6/215: 1 CD; 5 UC), high-grade dysplasia 3.7% (8/215) and low-grade dysplasia 7.9% (17/215). Lachnospira was decreased in IBD patients with cancer, while Agathobacter was decreased and Escherichia-Shigella increased in UC patients with any neoplasia. Bile acids were not associated with cancer or neoplasia. Unsupervised clustering identified three gut microbiota clusters in IBD patients associated with bile acid composition and clinical features, including a higher risk of neoplasia in UC in two clusters when compared to the third (relative risk (RR) 4.07 (95% CI 1.6-10.3, P < .01) and 3.56 (95% CI 1.4-9.2, P < .01)). In this multicentre observational study, a limited number of taxa were associated with neoplasia and exploratory microbiota clusters co-associated with clinical features, including neoplasia risk in UC. Given the very small number of cancers, the robustness of these findings will require assessment and validation in future studies.
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Affiliation(s)
- Aonghus Lavelle
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Stéphane Nancey
- Gastroenterology Department University Claude Bernard Lyon 1Hospices Civils de Lyon, CHU Lyon-Sud, Lyon, France
| | - Jean-Marie Reimund
- Hôpital de Hautpierre, CHU de Strasbourg, Service d’Hépato-gastroentérologie et Assistance Nutritive, Strasbourg, France
| | - David Laharie
- CHU de Bordeaux, Hôpital Haut-Lévêque, Service d’Hépato-gastroentérologie et oncologie digestive – Université de Bordeaux, Bordeaux, France
| | - Philippe Marteau
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Tenon Hospital, Paris, France
| | - Xavier Treton
- Gastroentérologie, MICI et Assistance Nutritive, DMU DIGEST, hôpital Beaujon, 100 bd du général Leclerc, Clichy, France
| | - Matthieu Allez
- Department of Hepato-Gastroenterology, Hôpital Saint-Louis, Paris, France
| | - Xavier Roblin
- Gastroenterology Department, CHU de Saint-Étienne - Hôpital Bellevue, St Etienne, France
| | - Georgia Malamut
- Gastroenterology Department, Hôpital Européen Georges-Pompidou, Paris, France
| | - Cyriane Oeuvray
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Nathalie Rolhion
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Xavier Dray
- Sorbonne University, Endoscopy Unit, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Dominique Rainteau
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Antonin Lamaziere
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Emilie Gauliard
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Julien Kirchgesner
- Paris Centre for Microbiome Medicine FHU, Paris, France,Department of Gastroenterology, Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Laurent Beaugerie
- Paris Centre for Microbiome Medicine FHU, Paris, France,Department of Gastroenterology, Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology, Nancy University Hospital, Nancy, France,Inserm NGERE, Université de Lorraine, Vandœuvre-Lès-Nancy, France,FHU Cure, Nancy, France
| | - Harry Sokol
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Paris, France,Paris Centre for Microbiome Medicine FHU, Paris, France,INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France,CONTACT Harry Sokol Gastroenterology Department, Hôpital Saint-Antoine, 184 rue du Faubourg Saint-Antoine, 75571Paris CEDEX 12, France
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12
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de Arruda JAA, Corrêa JD, Singh Y, Oliveira SR, Machado CC, Schneider AH, Medeiros JD, Fernandes GR, Macari S, Barrioni BR, Santos MDS, Duffles LF, Nakaya HTI, Fukada SY, Graves DT, Cunha FQ, Silva TA. Methotrexate promotes recovery of arthritis-induced alveolar bone loss and modifies the composition of the oral-gut microbiota. Anaerobe 2022; 75:102577. [PMID: 35490916 PMCID: PMC10782845 DOI: 10.1016/j.anaerobe.2022.102577] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/22/2022] [Accepted: 04/24/2022] [Indexed: 01/04/2023]
Abstract
OBJECTIVES The impact of rheumatoid arthritis (RA) on the shaping of the oral and gut microbiome raises the question of whether and how RA treatment modifies microbial communities. We examined changes in the oral and gut microbiota in a mouse model of antigen-induced arthritis (AIA) treated or not with methotrexate (MTX). METHODS Maxillae and stools were evaluated by the MiSeq platform of the V4 region of the 16S rRNA gene. Alveolar bone parameters were analysed by micro-computed tomography. Moreover, arthritis-induced changes in hyperalgesia and oedema were assessed, along with the impact on periodontal bone health. RESULTS Microbial communities in MTX-treated AIA mice revealed distinct clusters compared to the control and AIA groups. Overall, MTX impacted the richness and variability of microorganisms in the oral-gut axis microbiome at the phylum level. Regarding the oral microbiome, while in the control group the most dominant phylum was Firmicutes, in the AIA group there was a shift towards the predominance of Campilobacteriota and Bacteroidetes associated with the disease. MTX treatment led to greater dominance of the health-associated phylum Proteobacteria. In the gut microbiome, AIA induction resulted in increased abundance of the Verrucomicrobiota phylum, and MTX treatment restored its levels compared to control. Importantly, the MTX-treated AIA animals had significantly less periodontal bone loss, as well as decreased hyperalgesia and joint oedema compared to the AIA animals. CONCLUSION Data suggest the benefit of MTX treatment in protecting alveolar bone, in addition to providing new insights on the drug-microbiome interaction in the course of RA.
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Affiliation(s)
- José Alcides Almeida de Arruda
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jôice Dias Corrêa
- Department of Dentistry, Pontifical Catholic University, Belo Horizonte, MG, Brazil
| | - Youvika Singh
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sicília Rezende Oliveira
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caio Cavalcante Machado
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Ayda Henriques Schneider
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Julliane Dutra Medeiros
- Faculty of Biological and Agricultural Sciences, Mato Grosso State University, Alta Floresta, MT, Brazil
| | - Gabriel R Fernandes
- Oswaldo Cruz Fundation, René Rachou Research Center, Belo Horizonte, MG, Brazil
| | - Soraia Macari
- Department of Restorative Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Breno Rocha Barrioni
- Department of Metallurgical and Materials Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mariana de Souza Santos
- Department of Restorative Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Letícia Fernanda Duffles
- Department of BioMolecular Sciences, School of Pharmacological Science, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Helder Takashi Imoto Nakaya
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sandra Yasuyo Fukada
- Department of BioMolecular Sciences, School of Pharmacological Science, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Dana T Graves
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Fernando Queiroz Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Tarcília Aparecida Silva
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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13
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Schneider R, Kraljević M, Peterli R, Rohm TV, Bosch AJ, Low AJ, Keller L, AlAsfoor S, Häfliger S, Yilmaz B, Peterson CJ, Lazaridis II, Vonaesch P, Delko T, Cavelti-Weder C. Roux-en-Y gastric bypass with a long compared to a short biliopancreatic limb improves weight loss and glycemic control in obese mice. Surg Obes Relat Dis 2022; 18:1286-1297. [DOI: 10.1016/j.soard.2022.06.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022]
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14
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Tsakeng CUB, Tanekou TTM, Soffack SF, Tirados I, Noutchih C, Njiokou F, Bigoga JD, Wondji CS. Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment. Microorganisms 2022; 10:1141. [PMID: 35744659 PMCID: PMC9229743 DOI: 10.3390/microorganisms10061141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
The tsetse flies, biological vectors of African trypanosomes, harbour a variety of bacteria involved in their vector competence that may help in developing novel vector control tools. This study provides an inventory of tsetse bacterial communities in Cameroon and explores their possible associations with trypanosome establishment in Glossina palpalis palpalis. High throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene, with subsequent metagenomic, multivariate, and association analyses, were used to investigate the levels and patterns of microbial diversity in four tsetse species. Overall, 31 bacterial genera and four phyla were identified. The primary symbiont Wigglesworthia dominated almost all the samples, with an overall relative abundance of 47.29%, and seemed to be replaced by Serratia or Burkholderia in some G. tachinoides flies. Globally, significant differences were observed in the microbiome diversity and composition among tsetse species and between teneral and non-teneral flies, or between flies displaying or not displaying mature trypanosome infections. In addition, differential abundance testing showed some OTUs, or some bacteria taxa, associated with trypanosome maturation in tsetse flies. These bacteria could be further investigated for an understanding of their mechanism of action and alternatively, transformed and used to block trypanosome development in tsetse flies.
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Affiliation(s)
- Calmes Ursain Bouaka Tsakeng
- Centre for Research in Infectious Diseases (CRID), Yaoundé P.O. Box 13591, Cameroon; (C.U.B.T.); (C.N.); (F.N.); (C.S.W.)
- Department of Biochemistry, Faculty of Science, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Tito Tresor Melachio Tanekou
- Centre for Research in Infectious Diseases (CRID), Yaoundé P.O. Box 13591, Cameroon; (C.U.B.T.); (C.N.); (F.N.); (C.S.W.)
- Department of Biological Sciences, Faculty of Science, University of Bamenda, Bamenda P.O. Box 39, Cameroon
| | - Steve Feudjio Soffack
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Inaki Tirados
- Department of Vector Biology, Liverpool School of Tropical Medicine Pembroke Place, Liverpool L3 5QA, UK;
| | - Cedrique Noutchih
- Centre for Research in Infectious Diseases (CRID), Yaoundé P.O. Box 13591, Cameroon; (C.U.B.T.); (C.N.); (F.N.); (C.S.W.)
| | - Flobert Njiokou
- Centre for Research in Infectious Diseases (CRID), Yaoundé P.O. Box 13591, Cameroon; (C.U.B.T.); (C.N.); (F.N.); (C.S.W.)
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Jude Daiga Bigoga
- Department of Biochemistry, Faculty of Science, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Charles Sinclair Wondji
- Centre for Research in Infectious Diseases (CRID), Yaoundé P.O. Box 13591, Cameroon; (C.U.B.T.); (C.N.); (F.N.); (C.S.W.)
- Department of Vector Biology, Liverpool School of Tropical Medicine Pembroke Place, Liverpool L3 5QA, UK;
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15
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Microbial Communities in Underground Gas Reservoirs Offer Promising Biotechnological Potential. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Securing new sources of renewable energy and achieving national self-sufficiency in natural gas have become increasingly important in recent times. The study described in this paper focuses on three geologically diverse underground gas reservoirs (UGS) that are the natural habitat of methane-producing archaea, as well as other microorganisms with which methanogens have various ecological relationships. The objective of this research was to describe the microbial metabolism of methane in these specific anoxic environments during the year. DNA sequencing analyses revealed the presence of different methanogenic communities and their metabolic potential in all sites studied. Hydrogenotrophic Methanobacterium sp. prevailed in Lobodice UGS, members of the hydrogenotrophic order Methanomicrobiales predominated in Dolní Dunajovice UGS and thermophilic hydrogenotrophic members of the Methanothermobacter sp. were prevalent in Tvrdonice UGS. Gas composition and isotope analyses were performed simultaneously. The results suggest that the biotechnological potential of UGS for biomethane production cannot be neglected.
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16
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Karl CM, Vidakovic A, Pjevac P, Hausmann B, Schleining G, Ley JP, Berry D, Hans J, Wendelin M, König J, Somoza V, Lieder B. Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners. Front Nutr 2022; 9:831726. [PMID: 35694162 PMCID: PMC9174746 DOI: 10.3389/fnut.2022.831726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/23/2022] [Indexed: 12/05/2022] Open
Abstract
Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste (r = 0.3, p < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated (p < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): R2 = 0.76, p < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.
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Affiliation(s)
- Corinna M. Karl
- Christian Doppler Laboratory for Taste Research, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Ana Vidakovic
- Christian Doppler Laboratory for Taste Research, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Gerhard Schleining
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | - Jürgen König
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Veronika Somoza
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chair of Nutritional Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Barbara Lieder
- Christian Doppler Laboratory for Taste Research, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- *Correspondence: Barbara Lieder,
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17
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Hu J, Johnson TA, Zhang H, Cheng HW. The Microbiota-Gut-Brain Axis: Gut Microbiota Modulates Conspecific Aggression in Diversely Selected Laying Hens. Microorganisms 2022; 10:microorganisms10061081. [PMID: 35744601 PMCID: PMC9230770 DOI: 10.3390/microorganisms10061081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota plays an important role in regulating brain function, influencing psychological and emotional stability. The correlations between conspecific aggression, gut microbiota, and physiological homeostasis were further studied in inbred laying chicken lines, 63 and 72, which were diversely selected for Marek’s disease, and they also behave differently in aggression. Ten sixty-week-old hens from each line were sampled for blood, brain, and cecal content. Neurotransmitters, cytokines, corticosterone, and heterophil/lymphocyte ratios were determined. Cecal microbiota compositions were determined by bacterial 16s rRNA sequencing, and functional predictions were performed. Our data showed that the central serotonin and tryptophan levels were higher in line 63 compared to line 72 (p < 0.05). Plasma corticosterone, heterophil/lymphocyte ratios, and central norepinephrine were lower in line 63 (p < 0.05). The level of tumor necrosis factor α tended to be higher in line 63. Faecalibacterium, Oscillibacter, Butyricicoccus, and Bacteriodes were enriched in line 63 birds, while Clostridiales vadin BB60, Alistipes, Mollicutes RF39 were dominated in line 72. From the predicted bacterial functional genes, the kynurenine pathway was upregulated in line 72. These results suggested a functional linkage of the line differences in serotonergic activity, stress response, innate immunity, and gut microbiota populations.
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Affiliation(s)
- Jiaying Hu
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA;
| | - Timothy A. Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA;
- Correspondence: (T.A.J.); (H.-W.C.)
| | - Huanmin Zhang
- USDA-Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA;
| | - Heng-Wei Cheng
- USDA-Agricultural Research Service, Livestock Behavior Research Unit, West Lafayette, IN 47907, USA
- Correspondence: (T.A.J.); (H.-W.C.)
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18
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Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with
Brassica rapa
Growth. mSystems 2022; 7:e0006022. [PMID: 35575562 PMCID: PMC9239066 DOI: 10.1128/msystems.00060-22] [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] [Indexed: 11/20/2022] Open
Abstract
Microbial communities in the rhizosphere are distinct from those in soils and are influenced by stochastic and deterministic processes during plant development. These communities contain bacteria capable of promoting growth in host plants through various strategies. While some interactions are characterized in mechanistic detail using model systems, others can be inferred from culture-independent methods, such as 16S amplicon sequencing, using machine learning methods that account for this compositional data type. To characterize assembly processes and identify community members associated with plant growth amid the spatiotemporal variability of the rhizosphere, we grew Brassica rapa in a greenhouse time series with amended and reduced microbial treatments. Inoculation with a native soil community increased plant leaf area throughout the time series by up to 28%. Despite identifying spatially and temporally variable amplicon sequence variants (ASVs) in both treatments, inoculated communities were more highly connected and assembled more deterministically overall. Using a generalized linear modeling approach controlling for spatial variability, we identified 43 unique ASVs that were positively or negatively associated with leaf area, biomass, or growth rates across treatments and time stages. ASVs of the genus Flavobacterium dominated rhizosphere communities and showed some of the strongest positive and negative correlations with plant growth. Members of this genus, and growth-associated ASVs more broadly, exhibited variable connectivity in networks independent of growth association (positive or negative). These findings suggest host-rhizobacterial interactions vary temporally at narrow taxonomic scales and present a framework for identifying rhizobacteria that may work independently or in concert to improve agricultural yields. IMPORTANCE The rhizosphere, the zone of soil surrounding plant roots, is a hot spot for microbial activity, hosting bacteria capable of promoting plant growth in ways like increasing nutrient availability or fighting plant pathogens. This microbial system is highly diverse and most bacteria are unculturable, so to identify specific bacteria associated with plant growth, we used culture-independent community DNA sequencing combined with machine learning techniques. We identified 43 specific bacterial sequences associated with the growth of the plant Brassica rapa in different soil microbial treatments and at different stages of plant development. Most associations between bacterial abundances and plant growth were positive, although similar bacterial groups sometimes had different effects on growth. Why this happens will require more research, but overall, this study provides a way to identify native bacteria from plant roots that might be isolated and applied to boost agricultural yields.
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19
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Effect of Feeding Insoluble Fiber on the Microbiota and Metabolites of the Caecum and Feces of Rabbits Recovering from Epizootic Rabbit Enteropathy Relative to Non-Infected Rabbits. Pathogens 2022; 11:pathogens11050571. [PMID: 35631092 PMCID: PMC9146049 DOI: 10.3390/pathogens11050571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
This study aimed to investigate the effect of feeding insoluble fiber on the microbiota and metabolites of the caecum and feces of rabbits recovering from epizootic rabbit enteropathy relative to non-infected rabbits. Rabbits that had either recovered from epizootic rabbit enteropathy or ones that had never had epizootic rabbit enteropathy were fed on a diet of 32% or 36% neutral detergent fiber until they were 70 days of age. At this point, the short-chain fatty acid and ammonia levels were measured in caecotroph and fecal samples and compared using 2 × 2 ANOVA. The microbial composition of the samples was also analyzed using next-generation sequencing and compared by PERMANOVA. Caecotrophic samples from previously affected rabbits on lower fiber diets had higher short-chain fatty acid contents and higher species diversity index values for some indices (p < 0.05), although the fecal samples showed lower species diversity levels (p < 0.05). In addition, the PERMANOVA analyses demonstrated that differences were detected in the microbial composition of both fecal and caecotrophic samples, depending on the disease status at the outset of the experiment (p < 0.05). The results of this work show that, although there is some potential in the use of high-fiber diets for the treatment of rabbits that have had epizootic rabbit enteropathy, they are not able to produce the same digestive tract properties as those seen in rabbits that have never had the condition. This is true even after the rabbits have recovered from epizootic rabbit enteropathy.
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20
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Sommer AJ, Peters A, Rommel M, Cyrys J, Grallert H, Haller D, Müller CL, Bind MAC. A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota. PLoS Comput Biol 2022; 18:e1010044. [PMID: 35533202 PMCID: PMC9129050 DOI: 10.1371/journal.pcbi.1010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/24/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Statistical analysis of microbial genomic data within epidemiological cohort studies holds the promise to assess the influence of environmental exposures on both the host and the host-associated microbiome. However, the observational character of prospective cohort data and the intricate characteristics of microbiome data make it challenging to discover causal associations between environment and microbiome. Here, we introduce a causal inference framework based on the Rubin Causal Model that can help scientists to investigate such environment-host microbiome relationships, to capitalize on existing, possibly powerful, test statistics, and test plausible sharp null hypotheses. Using data from the German KORA cohort study, we illustrate our framework by designing two hypothetical randomized experiments with interventions of (i) air pollution reduction and (ii) smoking prevention. We study the effects of these interventions on the human gut microbiome by testing shifts in microbial diversity, changes in individual microbial abundances, and microbial network wiring between groups of matched subjects via randomization-based inference. In the smoking prevention scenario, we identify a small interconnected group of taxa worth further scrutiny, including Christensenellaceae and Ruminococcaceae genera, that have been previously associated with blood metabolite changes. These findings demonstrate that our framework may uncover potentially causal links between environmental exposure and the gut microbiome from observational data. We anticipate the present statistical framework to be a good starting point for further discoveries on the role of the gut microbiome in environmental health. Environmental influences on the human gut microbiome are still to be discovered or better understood. In this paper, we contribute to the field of microbiome research and environmental epidemiology by suggesting a stage-based causal inference framework relying on the foundations of the Rubin Causal Model. A particularity of the framework is the use of randomization-based inference, which we value to be a necessary exploratory inference method when tackling untapped research questions. To illustrate the framework, we explore the effects of two inhaled environmental exposures previously hypothesized to be linked with gastrointestinal diseases and the gut microbiome: air pollution exposure and cigarette smoking.
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Affiliation(s)
- Alice J. Sommer
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
- Institute for Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-University München, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- * E-mail: (AJS); (AP); (CLM)
| | - Annette Peters
- Institute for Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-University München, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (AJS); (AP); (CLM)
| | - Martina Rommel
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Josef Cyrys
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Christian L. Müller
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig-Maximilians-University München, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York City, New York, United States of America
- * E-mail: (AJS); (AP); (CLM)
| | - Marie-Abèle C. Bind
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
- Biostatistics Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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21
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Lin PC, Yang YCSH, Lin SC, Lu MC, Tsai YT, Lu SC, Chen SH, Chen SY. Clinical significance and intestinal microbiota composition in immunocompromised children with norovirus gastroenteritis. PLoS One 2022; 17:e0266876. [PMID: 35443009 PMCID: PMC9020708 DOI: 10.1371/journal.pone.0266876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/29/2022] [Indexed: 01/04/2023] Open
Abstract
Background Norovirus (NoV) infection is common in pediatric patients with immunodeficiency and is more likely to cause severe disease. Objective Our study aims to figure out the clinical differences and distribution of intestinal microbiota in immunocompromised children with NoV gastroenteritis. Methods Pediatric patients admitted to Shang-Ho Hospital with diagnosis of acute gastroenteritis including different immune status were enrolled and their medical records were reviewed. NoV gastroenteritis was validated using RT-PCR molecular methods. Viral shedding period was determined by real-time RT-PCR assays. Intestinal microbiota enrichment analysis was carried out by next generation sequencing after fecal DNA extraction and subsequent Linear Discriminant Analysis (LDA) Effect Size (LEfSe) method. Results Significantly higher frequency of diarrhea [mean, (IQR), 3.8 (3–5) /day] and longer viral shedding time [mean, IQR, 8.5 (5–13) days] was found in immunocompromised NoV infections than in immunocompetent patients without NoV infections (p = 0.013*) and immunocompetent patients with NoV infections (p = 0.030**). The fever prevalence was significantly lower in immunocompromised NoV infections than in different immune or infection status. Intestinal microbiota metagenomics analysis showed no significant community richness difference while the LEfSe analysis showed a significant difference in commensal richness at the phylum level, the family level, and the genus level in patients under different immune status. Conclusion We evaluated the clinical significances and microbiota composition in immunocompromised children with norovirus gastroenteritis. This will further facilitate studies of the interaction between the intestinal microbiota in such patients with precise determination of their bacterial infection control and probiotic supplements strategy.
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Affiliation(s)
- Pei-Chun Lin
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yu-Chen S. H. Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Chieh Lin
- Division of Allergy, Asthma and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Meng-Che Lu
- Division of Allergy, Asthma and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yin-Tai Tsai
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shou-Cheng Lu
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shu-Huey Chen
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
- * E-mail: (S-HC); , (S-YC)
| | - Shih-Yen Chen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
- * E-mail: (S-HC); , (S-YC)
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22
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Bibbal D, Ruiz P, Sapountzis P, Mazuy-Cruchaudet C, Loukiadis E, Auvray F, Forano E, Brugère H. Persistent Circulation of Enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Cattle Farms: Characterization of Enterohemorrhagic Escherichia coli O157:H7 Strains and Fecal Microbial Communities of Bovine Shedders and Non-shedders. Front Vet Sci 2022; 9:852475. [PMID: 35411306 PMCID: PMC8994043 DOI: 10.3389/fvets.2022.852475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Cattle are carriers, without clinical manifestations, of enterohemorrhagic Escherichia coli (EHEC) O157:H7 responsible for life-threatening infections in humans. A better identification of factors playing a role in maintaining persistence of such strains in cattle is required to develop more effective control measures. Hence, we conducted a study to identify farms with a persistent circulation of EHEC O157:H7. The EHEC O157:H7 herd status of 13 farms, which had previously provided bovine EHEC O157:H7 carriers at slaughter was investigated. Two farms were still housing positive young bulls, and this was true over a 1-year period. Only one fecal sample could be considered from a supershedder, and 60% of the carriers shed concentrations below 10 MPN/g. Moreover, EHEC O157:H7 represented minor subpopulations of E. coli. PFGE analysis of the EHEC O157:H7 strains showed that persistent circulation was due either to the persistence of a few predominant strains or to the repeated exposure of cattle to various strains. Finally, we compared fecal microbial communities of shedders (S) (n = 24) and non-shedders (NS) (n = 28), including 43 young bulls and nine cows, from one farm. Regarding alpha diversity, no significant difference between S vs. NS young bulls (n = 43) was observed. At the genus level, we identified 10 amplicon sequence variant (ASV) indicators of the S or NS groups. The bacterial indicators of S belonged to the family XIII UCG-001, Slackia, and Campylobacter genera, and Ruminococcaceae NK4A21A, Lachnospiraceae-UGC-010, and Lachnospiraceae-GCA-900066575 groups. The NS group indicator ASVs were affiliated to Pirellulaceae-1088-a5 gut group, Anaerovibrio, Victivallis, and Sellimonas genera. In conclusion, the characteristics enhancing the persistence of some predominant strains observed here should be explored further, and studies focused on mechanisms of competition among E. coli strains are also needed.
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Affiliation(s)
- Delphine Bibbal
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | | | - Christine Mazuy-Cruchaudet
- Université de Lyon, VetAgro Sup, National Reference Laboratory for E. coli (including VTEC), Marcy l'Etoile, France.,Université de Lyon, Laboratoire d'Ecologie Microbienne de Lyon, CNRS, INRAE, Université de Lyon 1, VetAgro Sup, Microbial Ecology Laboratory, Research Group on Bacterial Opportunistic Pathogens and Environment, Villeurbanne, France
| | - Estelle Loukiadis
- Université de Lyon, VetAgro Sup, National Reference Laboratory for E. coli (including VTEC), Marcy l'Etoile, France.,Université de Lyon, Laboratoire d'Ecologie Microbienne de Lyon, CNRS, INRAE, Université de Lyon 1, VetAgro Sup, Microbial Ecology Laboratory, Research Group on Bacterial Opportunistic Pathogens and Environment, Villeurbanne, France
| | - Frédéric Auvray
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | - Hubert Brugère
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
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23
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Rodríguez-Rodríguez JC, Bergeron Y, Kembel SW, Fenton NJ. Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses. Environ Microbiol 2022; 24:3517-3528. [PMID: 35416394 DOI: 10.1111/1462-2920.16013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/09/2022] [Accepted: 04/09/2022] [Indexed: 12/01/2022]
Abstract
The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species but may also be shaped by environmental conditions related with tree dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. The overall composition of moss phyllosphere was defined by the interaction of both factors, though most of bacterial phyla were determined by a strong effect of forest type. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the cyanobacteria family Nostocaceae differing the most between forest types. Our results advance the understanding of moss-associated microbial communities among coniferous and broadleaf deciduous forests, which are important with the increasing changes in tree dominance in the boreal system. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Juanita C Rodríguez-Rodríguez
- Forest Research Institute (IRF) , Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, QC J9X 5E4, Canada. 2 Département des sciences biologiques, Université du Québec à Montréal (UQAM), Montréal, QC, H2L 2C4, Canada
| | - Yves Bergeron
- Forest Research Institute (IRF) , Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, QC J9X 5E4, Canada. 2 Département des sciences biologiques, Université du Québec à Montréal (UQAM), Montréal, QC, H2L 2C4, Canada
| | | | - Nicole J Fenton
- Forest Research Institute (IRF) , Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, QC J9X 5E4, Canada. 2 Département des sciences biologiques, Université du Québec à Montréal (UQAM), Montréal, QC, H2L 2C4, Canada
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24
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Thirumalaisamy G, Malik PK, Trivedi S, Kolte AP, Bhatta R. Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep. Front Microbiol 2022; 13:780073. [PMID: 35369442 PMCID: PMC8964344 DOI: 10.3389/fmicb.2022.780073] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/27/2022] [Indexed: 11/30/2022] Open
Abstract
Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23–25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 107 cells/ml), Entodiniomorphs (× 107 cells/ml), and Holotrichs (× 106 cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.
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Affiliation(s)
- Govindasamy Thirumalaisamy
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India.,ICAR-National Dairy Research Institute, Karnal, India
| | - Pradeep Kumar Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | - Shraddha Trivedi
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | | | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, India
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25
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Molinero N, Taladrid D, Zorraquín-Peña I, de Celis M, Belda I, Mira A, Bartolomé B, Moreno-Arribas MV. Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis. Curr Issues Mol Biol 2022; 44:1513-1527. [PMID: 35723361 PMCID: PMC9164047 DOI: 10.3390/cimb44040103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/19/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.
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Affiliation(s)
- Natalia Molinero
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Diego Taladrid
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Irene Zorraquín-Peña
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Miguel de Celis
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain; (M.d.C.); (I.B.)
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain; (M.d.C.); (I.B.)
| | - Alex Mira
- Center for Advanced Research in Public Health, Department of Health and Genomics, FISABIO Foundation, 46020 Valencia, Spain;
| | - Begoña Bartolomé
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - M. Victoria Moreno-Arribas
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
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26
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Kracmarova M, Uhlik O, Strejcek M, Szakova J, Cerny J, Balik J, Tlustos P, Kohout P, Demnerova K, Stiborova H. Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic. ENVIRONMENTAL MICROBIOME 2022; 17:13. [PMID: 35346385 PMCID: PMC8962459 DOI: 10.1186/s40793-022-00406-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.
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Affiliation(s)
- Martina Kracmarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jindrich Cerny
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jiri Balik
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Pavel Tlustos
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Videnska 1083, 142 20, Praha 4, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Vinicna 5, 128 44, Praha 2, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N 6-carboxymethyllysine. Nat Neurosci 2022; 25:295-305. [PMID: 35241804 DOI: 10.1038/s41593-022-01027-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
Microglial function declines during aging. The interaction of microglia with the gut microbiota has been well characterized during development and adulthood but not in aging. Here, we compared microglial transcriptomes from young-adult and aged mice housed under germ-free and specific pathogen-free conditions and found that the microbiota influenced aging associated-changes in microglial gene expression. The absence of gut microbiota diminished oxidative stress and ameliorated mitochondrial dysfunction in microglia from the brains of aged mice. Unbiased metabolomic analyses of serum and brain tissue revealed the accumulation of N6-carboxymethyllysine (CML) in the microglia of the aging brain. CML mediated a burst of reactive oxygen species and impeded mitochondrial activity and ATP reservoirs in microglia. We validated the age-dependent rise in CML levels in the sera and brains of humans. Finally, a microbiota-dependent increase in intestinal permeability in aged mice mediated the elevated levels of CML. This study adds insight into how specific features of microglia from aged mice are regulated by the gut microbiota.
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Sertori R, Jones R, Basheer F, Rivera L, Dawson S, Loke S, Heidary S, Dhillon A, Liongue C, Ward AC. Generation and Characterization of a Zebrafish IL-2Rγc SCID Model. Int J Mol Sci 2022; 23:ijms23042385. [PMID: 35216498 PMCID: PMC8875600 DOI: 10.3390/ijms23042385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
The IL-2 family of cytokines act via receptor complexes that share the interleukin-2 receptor gamma common (IL-2Rγc) chain to play key roles in lymphopoiesis. Inactivating IL-2Rγc mutations results in severe combined immunodeficiency (SCID) in humans and other species. This study sought to generate an equivalent zebrafish SCID model. The zebrafish il2rga gene was targeted for genome editing using TALENs and presumed loss-of-function alleles analyzed with respect to immune cell development and impacts on intestinal microbiota and tumor immunity. Knockout of zebrafish Il-2rγc.a resulted in a SCID phenotype, including a significant reduction in T cells, with NK cells also impacted. This resulted in dysregulated intestinal microbiota and defective immunity to tumor xenotransplants. Collectively, this establishes a useful zebrafish SCID model.
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Affiliation(s)
- Robert Sertori
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
| | - Realla Jones
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
| | - Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Leni Rivera
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Samantha Dawson
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Stella Loke
- School of Life and Environmental Science, Deakin University, Burwood, VIC 3125, Australia;
| | - Somayyeh Heidary
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Amardeep Dhillon
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
- Correspondence:
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Pattaroni C, Macowan M, Chatzis R, Daunt C, Custovic A, Shields MD, Power UF, Grigg J, Roberts G, Ghazal P, Schwarze J, Gore M, Turner S, Bush A, Saglani S, Lloyd CM, Marsland BJ. Early life inter-kingdom interactions shape the immunological environment of the airways. MICROBIOME 2022; 10:34. [PMID: 35189979 PMCID: PMC8862481 DOI: 10.1186/s40168-021-01201-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/12/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns. RESULTS We found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance of Streptococcus species and Candida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns. CONCLUSION These data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health. TRIAL REGISTRATION NHS Health Research Authority, IRAS ID 199053. Registered 5 Oct 2016. https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/breathing-together/ Video abstract.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Matthew Macowan
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Roxanne Chatzis
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Carmel Daunt
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Adnan Custovic
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael D. Shields
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Ultan F. Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Jonathan Grigg
- Centre for Child Health, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham Roberts
- Human Development in Health School, University of Southampton Faculty of Medicine, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
| | - Peter Ghazal
- School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Jürgen Schwarze
- Centre for Inflammation Research, Child Life and Health, The University of Edinburgh, Edinburgh, UK
| | - Mindy Gore
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
- NHS Grampian, Aberdeen, UK
| | - Andrew Bush
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Sejal Saglani
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Clare M. Lloyd
- National Heart & Lung Institute, Imperial College London, London, UK
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Belevich TA, Milyutina IA. Species Diversity of Phototrophic Picoplankton in the Kara and Laptev Seas. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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31
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Tamargo A, Molinero N, Reinosa JJ, Alcolea-Rodriguez V, Portela R, Bañares MA, Fernández JF, Moreno-Arribas MV. PET microplastics affect human gut microbiota communities during simulated gastrointestinal digestion, first evidence of plausible polymer biodegradation during human digestion. Sci Rep 2022; 12:528. [PMID: 35017590 PMCID: PMC8752627 DOI: 10.1038/s41598-021-04489-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Microplastics (MPs) are a widely recognized global problem due to their prevalence in natural environments and the food chain. However, the impact of microplastics on human microbiota and their possible biotransformation in the gastrointestinal tract have not been well reported. To evaluate the potential risks of microplastics at the digestive level, completely passing a single dose of polyethylene terephthalate (PET) through the gastrointestinal tract was simulated by combining a harmonized static model and the dynamic gastrointestinal simgi model, which recreates the different regions of the digestive tract in physiological conditions. PET MPs started several biotransformations in the gastrointestinal tract and, at the colon, appeared to be structurally different from the original particles. We report that the feeding with microplastics alters human microbial colonic community composition and hypothesize that some members of the colonic microbiota could adhere to MPs surface promoting the formation of biofilms. The work presented here indicates that microplastics are indeed capable of digestive-level health effects. Considering this evidence and the increasing exposure to microplastics in consumer foods and beverages, the impact of plastics on the functionality of the gut microbiome and their potential biodegradation through digestion and intestinal bacteria merits critical investigation.
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Affiliation(s)
- Alba Tamargo
- Institute of Food Science Research, CIAL, CSIC-UAM, c/Nicolás Cabrera, 9, 28049, Madrid, Spain
| | - Natalia Molinero
- Institute of Food Science Research, CIAL, CSIC-UAM, c/Nicolás Cabrera, 9, 28049, Madrid, Spain
| | - Julián J Reinosa
- Instituto de Cerámica y Vidrio, CSIC, c/Kelsen, 5, 28049, Madrid, Spain
- Encapsulae S.L, c/Lituania 10, 12006, Castellón de la Plana, Spain
| | | | - Raquel Portela
- Institute of Catalysis and Petrochemistry, CSIC, C/Marie Curie, 2, 28049, Madrid, Spain
| | - Miguel A Bañares
- Institute of Catalysis and Petrochemistry, CSIC, C/Marie Curie, 2, 28049, Madrid, Spain
| | - Jose F Fernández
- Instituto de Cerámica y Vidrio, CSIC, c/Kelsen, 5, 28049, Madrid, Spain
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32
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From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada). Microorganisms 2022; 10:microorganisms10010129. [PMID: 35056578 PMCID: PMC8781179 DOI: 10.3390/microorganisms10010129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial communities play an important role in shallow terrestrial subsurface ecosystems. Most studies of this habitat have focused on planktonic communities that are found in the groundwater of aquifer systems and only target specific microbial groups. Therefore, a systematic understanding of the processes that govern the assembly of endolithic and sessile communities is still missing. This study aims to understand the effect of depth and biotic factors on these communities, to better unravel their origins and to compare their composition with the communities detected in groundwater. To do so, we collected samples from two profiles (~0–50 m) in aquifer sites in the Laurentians (Quebec, Canada), performed DNA extractions and Illumina sequencing. The results suggest that changes in geological material characteristics with depth represent a strong ecological and phylogenetical filter for most archaeal and bacterial communities. Additionally, the vertical movement of water from the surface plays a major role in shallow subsurface microbial assembly processes. Furthermore, biotic interactions between bacteria and eukaryotes were mostly positive which may indicate cooperative or mutualistic potential associations, such as cross-feeding and/or syntrophic relationships in the terrestrial subsurface. Our results also point toward the importance of sampling both the geological formation and groundwater when it comes to studying its overall microbiology.
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Peta V, Tantely LM, Potts R, Girod R, Pietri JE. A Francisella tularensis-Like Bacterium in Tropical Bed Bugs from Madagascar. Vector Borne Zoonotic Dis 2022; 22:58-61. [PMID: 34981990 DOI: 10.1089/vbz.2021.0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genus Francisella includes several highly virulent human pathogens and some tick endosymbionts. Francisella infections are acquired by humans through contact with vertebrate animal reservoirs or contaminated water or dust. The species Francisella tularensis can also be transmitted by arthropods including ticks, mosquitoes, and flies. For the first time, we describe the molecular detection of an F. tularensis-like bacterium in bed bugs from samples collected in rural Madagascar. This finding suggests a potential involvement of bed bugs in the ecology of Francisella. The role of bed bugs as possible hosts, reservoirs, or vectors of Francisella spp. should be further investigated.
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Affiliation(s)
- Vincent Peta
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Luciano M Tantely
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Rashaun Potts
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jose E Pietri
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
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Westaway JAF, Huerlimann R, Kandasamy Y, Miller CM, Norton R, Watson D, Infante-Vilamil S, Rudd D. To Probiotic or Not to Probiotic: A Metagenomic Comparison of the Discharge Gut Microbiome of Infants Supplemented With Probiotics in NICU and Those Who Are Not. Front Pediatr 2022; 10:838559. [PMID: 35345612 PMCID: PMC8957066 DOI: 10.3389/fped.2022.838559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/09/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Preterm birth is associated with the development of both acute and chronic disease, and the disruption of normal gut microbiome development. Recent studies have sought to both characterize and understand the links between disease and the microbiome. Probiotic treatment may correct for these microbial imbalances and, in turn, mitigate disease. However, the criteria for probiotic supplementation in NICU's in North Queensland, Australia limits its usage to the most premature (<32 weeks gestation) and small for gestational age infants (<1,500 g). Here we use a combination of amplicon and shotgun metagenomic sequencing to compare the gut microbiome of infants who fulfill the criteria for probiotic-treatment and those who do not. The aims of this study were to determine if probiotic-supplemented preterm infants have significantly different taxonomic and functional profiles when compared to non-supplemented preterm infants at discharge. METHODS Preterm infants were recruited in North Queensland, Australia, with fecal samples collected just prior to discharge (36 ± 0.5 weeks gestation), to capture potential changes that could be probiotic induced. All samples underwent 16S rRNA gene amplicon sequencing, with a subset also used for shotgun metagenomics. Mixed effects models were used to assess the effect of probiotics on alpha diversity, beta diversity and taxonomic abundance, whilst accounting for other known covariates. RESULTS Mixed effects modeling demonstrated that probiotic treatment had a significant effect on overall community composition (beta diversity), characterized by greater alpha diversity and differing abundances of several taxa, including Bifidobacterium and Lactobacillus, in supplemented infants. CONCLUSION Late preterm-infants who go without probiotic-supplementation may be missing out on stabilizing-effects provided through increased alpha diversity and the presence of commensal microbes, via the use of probiotic-treatment. These findings suggest that late-preterm infants may benefit from probiotic supplementation. More research is needed to both understand the consequences of the differences observed and the long-term effects of this probiotic-treatment.
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Affiliation(s)
- Jacob A F Westaway
- College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - Roger Huerlimann
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Onna, Japan.,Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Yoga Kandasamy
- College of Public Health, Medical and Veterinary Science, James Cook University, Townsville, QLD, Australia.,Neonatology, Townsville University Hospital, Townsville, QLD, Australia
| | - Catherine M Miller
- College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, QLD, Australia
| | - Robert Norton
- Microbiology, Pathology Queensland, Herston, QLD, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - David Watson
- Maternal-Fetal Medicine, Townsville University Hospital, Townsville, QLD, Australia
| | - Sandra Infante-Vilamil
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.,Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Donna Rudd
- College of Public Health, Medical and Veterinary Science, James Cook University, Townsville, QLD, Australia
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35
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Moynihan MA, Goodkin NF, Morgan KM, Kho PYY, Lopes Dos Santos A, Lauro FM, Baker DM, Martin P. Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef. THE ISME JOURNAL 2022; 16:233-246. [PMID: 34294880 PMCID: PMC8692400 DOI: 10.1038/s41396-021-01054-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N2 fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based 15N2 tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N2 fixation rates, DDN assimilation supplied up to 6% of the holobiont's N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N2 fixation rates were observed in the endolithic community (0.20 µg N cm-2 per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.
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Affiliation(s)
- Molly A Moynihan
- Earth Observatory of Singapore, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore.
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore.
| | - Nathalie F Goodkin
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- Earth Observatory of Singapore, Nanyang Technological University, Singapore, Singapore
- American Museum of Natural History, New York, NY, USA
| | - Kyle M Morgan
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Phyllis Y Y Kho
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | | | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - David M Baker
- Division for Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong, PR China
- The Swire Institute of Marine Science, University of Hong Kong, Hong Kong, PR China
| | - Patrick Martin
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
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Kasl BA, Machado VS, Henniger MT, Myer PR, Ballou MA. Feeding an acetate-based oral electrolyte reduces the ex vivo Escherichia coli growth potential in the abomasum of calves fed oral electrolytes alone or 30 minutes following a milk feeding when compared to feeding a bicarbonate-based oral electrolyte. J Dairy Sci 2021; 105:1542-1554. [PMID: 34955278 DOI: 10.3168/jds.2021-20939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022]
Abstract
Oral electrolyte solutions (OES) are a common, on-farm therapy to reestablish hydration and electrolyte balances in scouring and stressed calves. The objectives were to determine the effects of OES alkalinizing agent and the presence of a milk replacer feeding before OES administration on the abomasal environment in healthy Holstein calves. Abomasum cannulation was performed on 16 Holstein bull calves at 5 d of age. One calf was removed from the study before the calves were randomly assigned to treatments at 9 d of age. Treatments were arranged as a 2-by-2 factorial, with the following factors: oral electrolyte alkalinizing agent [acetate (A) or bicarbonate (B)] and liquid meal type milk replacer (MR) + OES (MR-A, MR-B), or OES only (OES-A, OES-B)]. The OES differed only by alkalinizing agent. On d 9, calves assigned to MR-A (n = 4) or MR-B (n = 4) received their morning MR aliquot 0.5 h before feeding 2 L of OES; the OES-A (n = 3) and OES-B (n = 4) treatment groups were fed 2 L of OES only. Peripheral blood samples and postprandial abomasal fluid samples were collected to assess abomasal pH, abomasal emptying rate (AER), and ex vivo abomasal Escherichia coli growth potential. Postprandial pH was greater in calves fed MR or B-based OES. Abomasal emptying rate was slower in calves receiving MR + OES, regardless of the alkalinizing agent. Ex vivo E. coli colony-forming unit counts were greater in calves fed either MR + OES or bicarbonate-based OES. Supplementing bicarbonate OES in addition to MR alters abomasal dynamics and may promote E. coli growth in postprandial abomasal fluid, partially due to sustained elevations in gastric pH and delayed gastric emptying rates. The OES containing sodium acetate limited ex vivo E. coli growth potential in abomasal fluid, thereby potentially reducing the risk of additional enteric bacterial complications associated with OES therapy.
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Affiliation(s)
- B A Kasl
- Department of Veterinary Sciences, Texas Tech University, Lubbock 79409
| | - V S Machado
- Department of Veterinary Sciences, Texas Tech University, Lubbock 79409
| | - M T Henniger
- Department of Animal Science, University of Tennessee, Knoxville 37996
| | - P R Myer
- Department of Animal Science, University of Tennessee, Knoxville 37996
| | - M A Ballou
- Department of Veterinary Sciences, Texas Tech University, Lubbock 79409.
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de Celis M, Serrano-Aguirre L, Belda I, Liébana-García R, Arroyo M, Marquina D, de la Mata I, Santos A. Acylase enzymes disrupting quorum sensing alter the transcriptome and phenotype of Pseudomonas aeruginosa, and the composition of bacterial biofilms from wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149401. [PMID: 34364277 DOI: 10.1016/j.scitotenv.2021.149401] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Biofilms represent an essential way of life and colonization of new environments for microorganisms. This feature is regulated by quorum sensing (QS), a microbial communication system based on autoinducer molecules, such as N-acyl-homoserine lactones (AHLs) in Gram negative bacteria. In artificial ecosystems, like Wastewater Treatment Plants (WWTPs), biofilm attachment in filtration membranes produces biofouling. In this environment, the microbial communities are mostly composed of Gram-negative phyla. Thus, we used two AHLs-degrading enzymes, obtained from Actinoplanes utahensis (namely AuAAC and AuAHLA) to determine the effects of degradation of QS signals in the biofilm formation, among other virulence factors, of a Pseudomonas aeruginosa strain isolated from a WWTP, assessing molecular mechanisms through transcriptomics. Besides, we studied the possible effects on community composition in biofilms from activated sludge samples. Although the studied enzymes only degraded the AHLs involved in one of the four QS systems of P. aeruginosa, these activities produced the deregulation of the complete QS network. In fact, AuAAC -the enzyme with higher catalytic efficiency- deregulated all the four QS systems. However, both enzymes reduced the biofilm formation and pyocyanin and protease production. The transcriptomic response of P. aeruginosa affected QS related genes, moreover, transcriptomic response to AuAAC affected mainly to QS related genes. Regarding community composition of biofilms, as expected, the abundance of Gram-negative phyla was significantly decreased after enzymatic treatment. These results support the potential use of such AHLs-degrading enzymes as a method to reduce biofilm formation in WWTP membranes and ameliorate bacterial virulence.
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Affiliation(s)
- M de Celis
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - L Serrano-Aguirre
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - I Belda
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - R Liébana-García
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - M Arroyo
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - D Marquina
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - I de la Mata
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - A Santos
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain.
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Kaiser-Thom S, Hilty M, Ramseyer A, Epper P, Gerber V. The relationship between equine pastern dermatitis, meteorological factors, and the skin microbiota. Vet Dermatol 2021; 33:165-e48. [PMID: 34888974 PMCID: PMC9300176 DOI: 10.1111/vde.13045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 08/11/2021] [Accepted: 09/01/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Equine pastern dermatitis (EPD) is a multifactorial syndrome, with prolonged exposure to moisture assumed to be a predisposing or primary factor. HYPOTHESIS/OBJECTIVES To examine the course of EPD lesion severity, changes in bacterial skin microbiota, and the influence of meteorological factors. ANIMALS Prospective, longitudinal cohort study over a one-year period, with six Franches-Montagnes stallions, four affected by EPD and two unaffected, that were kept under the same conditions. METHODS AND MATERIALS Pasterns were scored for lesion severity and sampled once a month for 12 consecutive months. Lesion severity, the skin microbiota and meteorological factors were examined for associations. RESULTS EPD lesions tended to worsen in autumn and at the beginning of spring. The relationship between lesion severity and the meteorological factor precipitation was not clearly evident; high scores were preceded by both low or high rates of precipitation. Microbiota in affected pasterns appeared to have experienced a reduction in alpha diversity. Beta diversity analyses demonstrated that bacterial community structures were altered in affected versus unaffected pasterns, and that alterations were more pronounced with higher EPD scores (P = 0.005). Meteorological factors also had considerable influences on the bacterial composition, whereby these influences appeared to be more marked in the affected pasterns (P = 0.001, F = 3.19) than in unaffected ones (P = 0.005, F = 1.83). CONCLUSIONS AND CLINICAL RELEVANCE Our study provides preliminary observations of the relationships between lesion severity, meteorological factors and cutaneous bacteria. The population was too small to draw firm conclusions, and further studies on environmental factors and the involvement of bacteria in this multifactorial disease are needed.
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Affiliation(s)
- Sarah Kaiser-Thom
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, Bern, 3010, Switzerland
| | - Alessandra Ramseyer
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland.,Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Les Longs-Prés, Avenches, 1580, Switzerland
| | - Pascale Epper
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland.,Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Les Longs-Prés, Avenches, 1580, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
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Snelders NC, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ. An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. Proc Natl Acad Sci U S A 2021; 118:e2110968118. [PMID: 34853168 PMCID: PMC8670511 DOI: 10.1073/pnas.2110968118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Microbes typically secrete a plethora of molecules to promote niche colonization. Soil-dwelling microbes are well-known producers of antimicrobials that are exploited to outcompete microbial coinhabitants. Also, plant pathogenic microbes secrete a diversity of molecules into their environment for niche establishment. Upon plant colonization, microbial pathogens secrete so-called effector proteins that promote disease development. While such effectors are typically considered to exclusively act through direct host manipulation, we recently reported that the soil-borne, fungal, xylem-colonizing vascular wilt pathogen Verticillium dahliae exploits effector proteins with antibacterial properties to promote host colonization through the manipulation of beneficial host microbiota. Since fungal evolution preceded land plant evolution, we now speculate that a subset of the pathogen effectors involved in host microbiota manipulation evolved from ancient antimicrobial proteins of terrestrial fungal ancestors that served in microbial competition prior to the evolution of plant pathogenicity. Here, we show that V. dahliae has co-opted an ancient antimicrobial protein as effector, named VdAMP3, for mycobiome manipulation in planta. We show that VdAMP3 is specifically expressed to ward off fungal niche competitors during resting structure formation in senescing mesophyll tissues. Our findings indicate that effector-mediated microbiome manipulation by plant pathogenic microbes extends beyond bacteria and also concerns eukaryotic members of the plant microbiome. Finally, we demonstrate that fungal pathogens can exploit plant microbiome-manipulating effectors in a life stage-specific manner and that a subset of these effectors has evolved from ancient antimicrobial proteins of fungal ancestors that likely originally functioned in manipulation of terrestrial biota.
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Affiliation(s)
- Nick C Snelders
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht 3584CH, The Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
| | - Gabriella C Petti
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht 3584CH, The Netherlands
| | - Bart P H J Thomma
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany;
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
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Host Factors Affect the Gut Microbiome More Significantly than Diet Shift. Microorganisms 2021; 9:microorganisms9122520. [PMID: 34946120 PMCID: PMC8707884 DOI: 10.3390/microorganisms9122520] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023] Open
Abstract
The determining factors of the composition of the gut microbiome are one of the main interests in current science. In this work, we compared the effect of diet shift (DS) from heavily relying on meatatarian diets to vegetarian diets and physical exercise (EX) on the composition of the gut microbiome after 3 months. Although both DS and EX affected the composition of the gut microbiome, the patterns of alteration were different. The α-diversity analyzed by InvSimpson, Shannon, Simpson, and Evenness showed that both EX and DS affected the microbiome, causing it to become more diverse, but EX affected the gut microbiome more significantly than DS. The β-diversity analyses indicated that EX and DS modified the gut microbiome in two different directions. Co-occurrence network analysis confirmed that both EX and DS modified the gut microbiome in different directions, although EX modified the gut microbiome more significantly. Most notably, the abundance of Dialister succinatiphilus was upregulated by EX, and the abundances of Bacteroides fragilis, Phascolarctobacterium faecium, and Megasphaera elsdenii were downregulated by both EX and DS. Overall, EX modulated the composition of the gut microbiome more significantly than DS, meaning that host factors are more important in determining the gut microbiome than diets. This work also provides a new theoretical basis for why physical exercise is more health-beneficial than vegetarian diets.
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Kiama CW, Njire MM, Kambura AK, Mugweru JN, Matiru VN, Wafula EN, Kagali RN, Kuja JO. Prokaryotic diversity and composition within equatorial lakes Olbolosat and Oloiden in Kenya (Africa). CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100066. [PMID: 34841356 PMCID: PMC8610316 DOI: 10.1016/j.crmicr.2021.100066] [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] [Received: 05/28/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 01/04/2023] Open
Abstract
Total community 16S rDNA was used to determine the diversity and composition of bacteria and archaea within lakes Olbolosat and Oloiden in Kenya. The V3-V4 hypervariable region of the 16S rRNA gene was targeted since it's highly conserved and has a higher resolution for lower rank taxa. High throughput sequencing was performed on 15 samples obtained from the two lakes using the Illumina Miseq platform. Lakes Olbolosat and Oloiden shared 280 of 10,523 Amplicon Sequence Variants (ASVs) recovered while the four sample types (water, microbial mats, dry and wet sediments) shared 4 ASVs. The composition of ASVs in lake Olbolosat was highly dependent on Cu+, Fe2+, NH4 +, and Mn2+, while L. Oloiden was dependent on Mg2+, Na+, Ca2+, and K+. All the alpha diversity indices except Simpson were highest in the dry sediment sample (EC1 and 2) both from lake Oloiden. The abundant phyla included Proteobacteria (33.8%), Firmicutes (27.3%), Actinobacteriota (21.2%), Chloroflexi (6.8%), Cyanobacteria (3.8%), Acidobacteriota (2.8%), Planctomycetota (1.9%) and Bacteroidota (1.1%). Analysis of similarity (ANOSIM) revealed a significant difference in ASV composition between the two lakes (r = 0.191, p = 0.048), and between the sample types (r = 0.6667, p = 0.001). The interaction network for prokaryotic communities within the two lakes displayed Proteobacteria to be highly positively connected with other microbes. PERMANOVA results suggest that temperature controls the functioning of the two ecosystems.
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Affiliation(s)
- Catherine Wachera Kiama
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Moses Mucugi Njire
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Anne Kelly Kambura
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300 Voi, Kenya
| | | | - Viviene Njeri Matiru
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Eliud Nalianya Wafula
- Department of Physical and Biological Sciences, Bomet University College, P.O Box 701-20400, Bomet Kenya
| | - Robert Nesta Kagali
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Josiah Ochieng Kuja
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
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Goelz H, Wetzel S, Mehrbarzin N, Utzolino S, Häcker G, Badr MT. Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients. Cells 2021; 10:3226. [PMID: 34831447 PMCID: PMC8617993 DOI: 10.3390/cells10113226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients. Owing to a relatively low success rate of conventional culture methods in identifying the responsible pathogens, new methods may be helpful to guide antimicrobial therapy and to refine empirical regimens. Here, we aim to assess outcomes and to identify responsible pathogens in ascitic fluid infections, in order to improve patients' care and to guide empirical therapy. METHODS Between October 2019 and March 2021, we prospectively collected 50 ascitic fluid samples from ICU patients with suspected infection. Beside standard culture-based microbiology methods, excess fluid underwent DNA isolation and was analyzed by next- and third-generation sequencing (NGS) methods. RESULTS NGS-based methods had higher sensitivity in detecting additional pathogenic bacteria such as E. faecalis and Klebsiella in 33 out of 50 (66%) ascitic fluid samples compared with culture-based methods (26%). Anaerobic bacteria were especially identified by sequencing-based methods in 28 samples (56%), in comparison with only three samples in culture. Analysis of clinical data showed a correlation between sequencing results and various clinical parameters such as peritonitis and hospitalization outcomes. CONCLUSIONS Our results show that, in ascitic fluid infections, NGS-based methods have a higher sensitivity for the identification of clinically relevant pathogens than standard microbiological culture diagnostics, especially in detecting hard-to-culture anaerobic bacteria. Patients with such infections may benefit from the use of NGS methods by the possibility of earlier and better targeted antimicrobial therapy, which has the potential to lower the high morbidity and mortality in critically ill patients with ascitic bacterial infection.
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Affiliation(s)
- Hanna Goelz
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Stefan Utzolino
- Center of Surgery, Department of General and Visceral Surgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
- IMM-PACT-Program, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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Enaud R, Cambos S, Viaud E, Guichoux E, Chancerel E, Marighetto A, Etchamendy N, Clark S, Mohammedi K, Cota D, Delhaes L, Gatta-Cherifi B. Gut Microbiota and Mycobiota Evolution Is Linked to Memory Improvement after Bariatric Surgery in Obese Patients: A Pilot Study. Nutrients 2021; 13:nu13114061. [PMID: 34836316 PMCID: PMC8620125 DOI: 10.3390/nu13114061] [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: 10/16/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Abstract
Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia, Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.
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Affiliation(s)
- Raphaël Enaud
- Centre Hospitalier de Bordeaux, CRCM Pédiatrique, CIC 1401, 33000 Bordeaux, France;
- Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Hôpital Xavier Arnozan, University of Bordeaux, Avenue du Haut Lévêque, 33604 Pessac, France;
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU ACRONIM, 33000 Bordeaux, France;
| | - Sophie Cambos
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France;
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Esther Viaud
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Erwan Guichoux
- BIOGECO, INRAE, University of Bordeaux, 69 route d’Arcachon, 33610 Cestas, France; (E.G.); (E.C.)
| | - Emilie Chancerel
- BIOGECO, INRAE, University of Bordeaux, 69 route d’Arcachon, 33610 Cestas, France; (E.G.); (E.C.)
| | - Aline Marighetto
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Nicole Etchamendy
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Samantha Clark
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Kamel Mohammedi
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU ACRONIM, 33000 Bordeaux, France;
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France;
| | - Daniela Cota
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU TALISMENT, 33000 Bordeaux, France
| | - Laurence Delhaes
- Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Hôpital Xavier Arnozan, University of Bordeaux, Avenue du Haut Lévêque, 33604 Pessac, France;
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU ACRONIM, 33000 Bordeaux, France;
| | - Blandine Gatta-Cherifi
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France;
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU TALISMENT, 33000 Bordeaux, France
- Correspondence:
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Distinct methane-dependent biogeochemical states in Arctic seafloor gas hydrate mounds. Nat Commun 2021; 12:6296. [PMID: 34728618 PMCID: PMC8563959 DOI: 10.1038/s41467-021-26549-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/27/2021] [Indexed: 01/04/2023] Open
Abstract
Archaea mediating anaerobic methane oxidation are key in preventing methane produced in marine sediments from reaching the hydrosphere; however, a complete understanding of how microbial communities in natural settings respond to changes in the flux of methane remains largely uncharacterized. We investigate microbial communities in gas hydrate-bearing seafloor mounds at Storfjordrenna, offshore Svalbard in the high Arctic, where we identify distinct methane concentration profiles that include steady-state, recently-increasing subsurface diffusive flux, and active gas seepage. Populations of anaerobic methanotrophs and sulfate-reducing bacteria were highest at the seep site, while decreased community diversity was associated with a recent increase in methane influx. Despite high methane fluxes and methanotroph doubling times estimated at 5-9 months, microbial community responses were largely synchronous with the advancement of methane into shallower sediment horizons. Together, these provide a framework for interpreting subseafloor microbial responses to methane escape in a warming Arctic Ocean.
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Aslam H, Collier F, Davis JA, Quinn TP, O'Hely M, Pasco JA, Jacka FN, Loughman A. Gut Microbiome Diversity and Composition Are Associated with Habitual Dairy Intakes: A Cross-Sectional Study in Men. J Nutr 2021; 151:3400-3412. [PMID: 34386821 DOI: 10.1093/jn/nxab252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/09/2021] [Accepted: 07/07/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND At a population level, the relation between dairy consumption and gut microbiome composition is poorly understood. OBJECTIVES We sought to study the cross-sectional associations between individual dairy foods (i.e., milk, yogurt, and cheese), as well as total dairy intake, and the gut microbiome composition in a large, representative sample of men living in south-eastern Australia. METHODS Data on 474 men (mean ± SD: 64.5 ± 13.5 y old) from the Geelong Osteoporosis Study were used to assess the cross-sectional association between dairy consumption and gut microbiome. Information on dairy intake was self-reported. Men were categorized as consumers and nonconsumers of milk, yogurt, cheese, and high- and low-fat milk. Milk, yogurt, and cheese intakes were summed to calculate the total dairy consumed per day and categorized into either low (<2.5 servings/d) or high (≥2.5 servings/d) total dairy groups. Fecal samples were analyzed using bacterial 16S ribosomal RNA (rRNA) gene sequencing. After assessment of α and β diversity, differential abundance analysis was performed to identify bacterial taxa associated with each of milk, yogurt, and cheese consumption compared with nonconsumption, low compared with high total dairy, and low- compared with high-fat milk consumption. All analyses were adjusted for potential confounders. RESULTS α Diversity was not associated with consumption of any of the dairy groups. Differences in β diversity were observed between milk and yogurt consumption compared with nonconsumption. Taxa belonging to the genera Ruminococcaceae UCG-010 and Bifidobacterium showed negative and weak positive associations with milk consumption, respectively. A taxon from the genus Streptococcus was positively associated with yogurt consumption, whereas a taxon from the genus Eisenbergiella was negatively associated with cheese consumption. No specific taxa were associated with low- compared with high-fat milk nor low compared with high total dairy consumption. CONCLUSIONS In men, community-level microbiome differences were observed between consumers and nonconsumers of milk and yogurt. Bacterial taxon-level associations were detected with milk, yogurt, and cheese consumption. Total dairy consumption was not associated with any microbiome measures, suggesting that individual dairy foods may have differential roles in shaping the gut microbiome in men.
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Affiliation(s)
- Hajara Aslam
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia
| | - Fiona Collier
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia.,Barwon Health, Geelong, Victoria, Australia
| | - Jessica A Davis
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia
| | - Thomas P Quinn
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Victoria, Australia
| | - Martin O'Hely
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Julie A Pasco
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia.,Barwon Health, Geelong, Victoria, Australia.,Department of Medicine-Western Health, Melbourne Medical School, The University of Melbourne, St Albans, Victoria, Australia
| | - Felice N Jacka
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia.,Centre for Adolescent Health, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Black Dog Institute, Sydney, New South Wales, Australia.,Biomedical Sciences, James Cook University , Douglas, Queensland, Australia
| | - Amy Loughman
- IMPACT-the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University and Barwon Health, Geelong, Victoria, Australia
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Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K. Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. THE ISME JOURNAL 2021; 15:3159-3180. [PMID: 33981000 PMCID: PMC8528874 DOI: 10.1038/s41396-021-00992-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.
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Affiliation(s)
- Mathias Flieder
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Joy Buongiorno
- grid.411461.70000 0001 2315 1184Department of Microbiology, University of Tennessee, Knoxville, TN USA ,grid.421147.50000 0000 8528 5498Present Address: Division of Natural Sciences, Maryville College, Maryville, TN USA
| | - Craig W. Herbold
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- grid.10420.370000 0001 2286 1424Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Karen G. Lloyd
- grid.411461.70000 0001 2315 1184Department of Microbiology, University of Tennessee, Knoxville, TN USA
| | - Alexander Loy
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria ,grid.465498.2Austrian Polar Research Institute, Vienna, Austria
| | - Kenneth Wasmund
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.465498.2Austrian Polar Research Institute, Vienna, Austria ,grid.5117.20000 0001 0742 471XCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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47
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Hegg A, Radersma R, Uller T. A field experiment reveals seasonal variation in the
Daphnia
gut microbiome. OIKOS 2021. [DOI: 10.1111/oik.08530] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Reinder Radersma
- Dept of Biology, Lund Univ. Lund Sweden
- Centrum Wiskunde&Informatica Amsterdam the Netherlands
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Seki D, Mayer M, Hausmann B, Pjevac P, Giordano V, Goeral K, Unterasinger L, Klebermaß-Schrehof K, De Paepe K, Van de Wiele T, Spittler A, Kasprian G, Warth B, Berger A, Berry D, Wisgrill L. Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage. Cell Host Microbe 2021; 29:1558-1572.e6. [PMID: 34480872 PMCID: PMC8525911 DOI: 10.1016/j.chom.2021.08.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023]
Abstract
Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics. We found that maturation of electrocortical activity is suppressed in infants with severe brain damage. This is accompanied by elevated γδ T cell levels and increased T cell secretion of vascular endothelial growth factor and reduced secretion of neuroprotectants. Notably, Klebsiella overgrowth in the gut is highly predictive for brain damage and is associated with a pro-inflammatory immunological tone. These results suggest that aberrant development of the gut-microbiota-immune-brain axis may drive or exacerbate brain injury in extremely premature neonates and represents a promising target for novel intervention strategies.
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Affiliation(s)
- David Seki
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Margareta Mayer
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria
| | - Vito Giordano
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Katharina Goeral
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Unterasinger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Katrin Klebermaß-Schrehof
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Kim De Paepe
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, 9000 Ghent, Belgium
| | - Tom Van de Wiele
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, 9000 Ghent, Belgium
| | - Andreas Spittler
- Core Facility Flow Cytometry & Department of Surgery, Research Lab, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Radiology, Medical University of Vienna, 1090 Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Austria
| | - Angelika Berger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria.
| | - Lukas Wisgrill
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria.
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Virginio Junior GF, Reis ME, da Silva AP, de Toledo AF, Cezar AM, Mendes LW, Greco L, Montenegro H, Coutinho LL, Bittar CMM. Does algae β-glucan affect the fecal bacteriome in dairy calves? PLoS One 2021; 16:e0258069. [PMID: 34591937 PMCID: PMC8483308 DOI: 10.1371/journal.pone.0258069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
β-glucans has been reported to be associated with many health-promoting and improvements in animal performance, however, information about their effects on the bacterial community remains unknown. This study aimed to investigate how the addition of β-glucans can affect the fecal bacterial community with possible consequences on animal growth and health. For this, newborn Holstein calves (n = 14) were individually housed in tropical shelters and blocked according to sex, date, and weight at birth and randomly assigned to one of the following treatments: (1) Control: milk replacer (14% solids, 24% CP, 18.5% fat); (2) β-glucans: milk replacer supplemented with β-glucans (2 g/d). All calves were bucket fed 6 L/d of milk replacer and received water and starter concentrate ad libitum starting on d 2. To evaluate the bacteriome, fecal samples were collected at weeks 1, 2, 4, and 8. The bacterial community was assessed through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. No differences for Shannon and Chao1 indexes were observed for treatments, but both indexes increased with age (P < 0.001). There were dissimilarities in the structure of the bacterial community during the pre-weaning period (P = 0.01). In a deeper taxonomic level, Collinsella (Actinobacteriota), Prevotella (Bacteroidota), and Lactobacillus (Firmicutes) were the most abundant genera (9.84, 9.54, and 8.82% of the sequences, respectively). β-glucans promoted a higher abundance of Alloprevotella and Holdemanella, which may indicate a beneficial effect of supplementation on dairy calves. The bacterial community was highly correlated with the fecal score at weeks 1 and 2 and with starter concentrate intake at week 8. In conclusion, algae β-glucan supplementation could be beneficial to fecal bacteriome and consequently to the health and performance of dairy calves.
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Affiliation(s)
- Gercino Ferreira Virginio Junior
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (GFVJ); (CMMB)
| | - Maria Eduarda Reis
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Ana Paula da Silva
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Ariany Faria de Toledo
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Amanda Moelemberg Cezar
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Leandro Greco
- Kemin Animal Nutrition and Health Division South America, Valinhos, São Paulo, Brazil
| | - Horácio Montenegro
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Carla Maris Machado Bittar
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (GFVJ); (CMMB)
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50
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Dal Bello M, Lee H, Goyal A, Gore J. Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism. Nat Ecol Evol 2021; 5:1424-1434. [PMID: 34413507 DOI: 10.1038/s41559-021-01535-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/14/2021] [Indexed: 02/06/2023]
Abstract
The relationship between the number of available nutrients and community diversity is a central question in ecological research that remains unanswered. Here we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.
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Affiliation(s)
- Martina Dal Bello
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Hyunseok Lee
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeff Gore
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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