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Cibulková I, Řehořová V, Wilhelm M, Soukupová H, Hajer J, Duška F, Daňková H, Cahová M. Evaluating Bacterial Viability in Faecal Microbiota Transplantation: A Comparative Analysis of In Vitro Cultivation and Membrane Integrity Methods. J Clin Lab Anal 2024:e25105. [PMID: 39360586 DOI: 10.1002/jcla.25105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/03/2024] [Accepted: 09/08/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Faecal microbiota transplantation (FMT) is a developing therapy for disorders related to gut dysbiosis. Despite its growing application, standardised protocols for FMT filtrate preparation and quality assessment remain undeveloped. The viability of bacteria in the filtrate is crucial for FMT's efficacy and for validating protocol execution. We compared two methods-in vitro cultivation and membrane integrity assessment-for their accuracy, reproducibility and clinical applicability in measuring bacterial viability in frozen FMT stool filtrate. METHODS Bacterial viability in stool filtrate was evaluated using (i) membrane integrity through fluorescent DNA staining with SYTO9 and propidium iodide, followed by flow cytometry and (ii) culturable bacteria counts (colony-forming units, CFU) under aerobic or anaerobic conditions. RESULTS Using different types of samples (pure bacterial culture, stool of germ-free and conventionally bred mice, native and heat-treated human stool), we refined the bacterial DNA staining protocol integrated with flow cytometry for assessment of bacterial viability in frozen human stool samples. Both the membrane integrity-based and cultivation-based methods exhibited significant variability in bacterial viability across different FMT filtrates, without correlation. The cultivation-based method showed a mean coefficient of variance of 30.3%, ranging from 7.4% to 60.1%. Conversely, the membrane integrity approach yielded more reproducible results, with a mean coefficient of variance for viable cells of 6.4% ranging from 0.2% to 18.2%. CONCLUSION Bacterial viability assessment in stool filtrate using the membrane integrity method offers robust and precise data, making it a suitable option for faecal material evaluation in FMT. In contrast, the cultivation-dependent methods produce inconsistent outcomes.
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Affiliation(s)
- Ivana Cibulková
- Division of Gastroenterology, Department of Internal Medicine, Kralovske Vinohrady University Hospital, Prague, Czech Republic
- The Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Řehořová
- The Third Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Anaesthesia and Intensive Care Medicine, Kralovske Vinohrady University Hospital, Prague, Czech Republic
| | - Marek Wilhelm
- The Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hana Soukupová
- The Third Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Microbiology, Kralovske Vinohrady University Hospital, Prague, Czech Republic
| | - Jan Hajer
- Division of Gastroenterology, Department of Internal Medicine, Kralovske Vinohrady University Hospital, Prague, Czech Republic
- The Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - František Duška
- The Third Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Anaesthesia and Intensive Care Medicine, Kralovske Vinohrady University Hospital, Prague, Czech Republic
| | - Helena Daňková
- Department of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Monika Cahová
- Department of Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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Mancin L, Paoli A, Berry S, Gonzalez JT, Collins AJ, Lizarraga MA, Mota JF, Nicola S, Rollo I. Standardization of gut microbiome analysis in sports. Cell Rep Med 2024:101759. [PMID: 39368478 DOI: 10.1016/j.xcrm.2024.101759] [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: 05/14/2024] [Revised: 08/09/2024] [Accepted: 09/10/2024] [Indexed: 10/07/2024]
Abstract
The gut microbiome plays a significant role in physiological functions such as nutrient processing, vitamin production, inflammatory response, and immune modulation, which, in turn, are important contributors to athlete health and performance. To date, the interpretation, discussion, and visualization of microbiome results of athletes are challenging, due to a lack of standard parameters and reference data for collection and comparison. The purpose of this perspective piece is to provide researchers with an easy-to-understand framework for the collection, analysis, and data management related to the gut microbiome with a specific focus on athletic populations. In the absence of a consensus on microbiome research in the sports field, we hope that these considerations serve as foundational "best practice." Adherence to these standard operating procedures will accelerate the path toward improving the quality of data and ultimately our understanding of the influence of the gut microbiome in sport settings.
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Affiliation(s)
- Laura Mancin
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Human Inspired Technology Research Center HIT, University of Padua, Padua, Italy.
| | - Antonio Paoli
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Human Inspired Technology Research Center HIT, University of Padua, Padua, Italy
| | - Sara Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | | | - Adam J Collins
- Department for Health, University of Bath, BA2 7AY Bath, UK
| | | | - Joao Felipe Mota
- APC Microbiome Ireland, Department of Medicine, School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Segata Nicola
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Ian Rollo
- Gatorade Sports Science Institute, PepsiCo Life Sciences, Global R&D, Leicestershire, UK; School of Sports Exercise and Health Sciences, Loughborough University, Leicestershire, UK
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Long AE, Pitta D, Hennessy M, Indugu N, Vecchiarelli B, Luethy D, Aceto H, Hurcombe S. Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses. BMC Vet Res 2024; 20:306. [PMID: 38987780 PMCID: PMC11234551 DOI: 10.1186/s12917-024-04166-w] [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: 03/13/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Currently, lack of standardization for fecal microbiota transplantation (FMT) in equine practice has resulted in highly variable techniques, and there is no data on the bacterial metabolic activity or viability of the administered product. The objectives of this study were to compare the total and potentially metabolically active bacterial populations in equine FMT, and assess the effect of different frozen storage times, buffers, and temperatures on an equine FMT product. Fresh feces collected from three healthy adult horses was subjected to different storage methods. This included different preservation solutions (saline plus glycerol or saline only), temperature (-20 °C or -80 °C), and time (fresh, 30, 60, or 90 days). Samples underwent DNA extraction to assess total bacterial populations (both live and dead combined) and RNA extraction followed by reverse transcription to cDNA as a proxy to assess viable bacteria, then 16s rRNA gene amplicon sequencing using the V1-V2 region. RESULTS The largest difference in population indices and taxonomic composition at the genus level was seen when evaluating the results of DNA-based (total) and cDNA-based (potentially metabolically active) extraction method. At the community level, alpha diversity (observed species, Shannon diversity) was significantly decreased in frozen samples for DNA-based analysis (P < 0.05), with less difference seen for cDNA-based sequencing. Using DNA-based analysis, length of storage had a significant impact (P < 0.05) on the bacterial community profiles. For potentially metabolically active populations, storage overall had less of an effect on the bacterial community composition, with a significant effect of buffer (P < 0.05). Individual horse had the most significant effect within both DNA and cDNA bacterial communities. CONCLUSIONS Frozen storage of equine FMT material can preserve potentially metabolically active bacteria of the equine fecal microbiome, with saline plus glycerol preservation more effective than saline alone. Larger studies are needed to determine if these findings apply to other individual horses. The ability to freeze FMT material for use in equine patients could allow for easier clinical use of fecal transplant in horses with disturbances in their intestinal microbiome.
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Affiliation(s)
- Alicia E Long
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA.
| | - Dipti Pitta
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Meagan Hennessy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Nagaraju Indugu
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Daniela Luethy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Helen Aceto
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Samuel Hurcombe
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
- Veterinary Innovative Partners, New York, NY, USA
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Kacerovsky M, Hornychova H, Jaiman S, Pavlikova L, Holeckova M, Jacobsson B, Tsiartas P, Musilova I. Angiogenic imbalance in pregnancies with preterm prelabor rupture of membranes between 34 and 37 weeks of gestation. Acta Obstet Gynecol Scand 2024; 103:1120-1131. [PMID: 38511515 PMCID: PMC11103135 DOI: 10.1111/aogs.14833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION This study aimed to identify whether microbial invasion of the amniotic cavity and/or intra-amniotic inflammation in women with late preterm prelabor rupture of membranes (PPROM) was associated with changes in concentrations of soluble fms-like tyrosine kinase-1 (sFlt-1), placental growth factor (PlGF) and its ratio in maternal serum, and whether placental features consistent with maternal vascular malperfusion further affect their concentrations. MATERIAL AND METHODS This historical study included 154 women with singleton pregnancies complicated by PPROM between gestational ages 34+0 and 36+6 weeks. Transabdominal amniocentesis was performed as part of standard clinical management to evaluate the intra-amniotic environment. Women were categorized into two subgroups based on the presence of microorganisms and/or their nucleic acids in amniotic fluid (determined by culturing and molecular biology method) and intra-amniotic inflammation (by amniotic fluid interleukin-6 concentration evaluation): (1) those with the presence of microorganisms and/or inflammation (at least one present) and (2) those with negative amniotic fluid for infection/inflammation (absence of both). Concentrations of sFlt-1 and PlGF were assessed using the Elecsys® sFlt-1 and Elecsys® PlGF immunoassays and converted into multiples of medians. RESULTS Women with the presence of microorganisms and/or inflammation in amniotic fluid had lower serum concentrations of sFlt-1 and sFlt-1/PlGF ratios and higher concentrations of PlGF compared with those with negative amniotic fluid. (sFlt-1: presence: median 1.0 multiples of the median (MoM), vs negative: median: 1.5 MoM, P = 0.003; PlGF: presence: median 0.7 MoM, vs negative: median 0.4 MoM, P = 0.02; sFlt-1/PlGF: presence: median 8.9 vs negative 25.0, P = 0.001). Higher serum concentrations of sFlt-1 and sFlt-1/PlGF ratios as well as lower concentrations of PlGF were found in the subsets of women with maternal vascular malperfusion than in those without maternal vascular malperfusion. CONCLUSIONS Among women experiencing late PPROM, angiogenic imbalance in maternal serum is primarily observed in those without both microbial invasion of the amniotic cavity and intra-amniotic inflammation. Additionally, there is an association between angiogenic imbalance and the presence of maternal vascular malperfusion.
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Affiliation(s)
- Marian Kacerovsky
- Biomedical Research CenterUniversity Hospital Hradec KraloveHradec KraloveCzech Republic
- Department of Obstetrics and GynecologyHospital MostUsti nad LabemCzech Republic
| | - Helena Hornychova
- Fingerland Institute of PathologyUniversity Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec KraloveHradec KraloveCzech Republic
| | - Sunil Jaiman
- Department of Pathology, School of Medicine DetroitWayne State UniversityDetroitMichiganUSA
| | - Ladislava Pavlikova
- Institute of Clinical Biochemistry and DiagnosticsUniversity Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec KraloveHradec KraloveCzech Republic
| | - Magdalena Holeckova
- Institute of Clinical Biochemistry and DiagnosticsUniversity Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec KraloveHradec KraloveCzech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
- Department of Obstetrics and Gynecology, Region Västra GötalandSahlgrenska University HospitalGothenburgSweden
- Department of Genetics and Bioinformatics, Domain of Health Data and DigitalizationInstitute of Public HealthOsloNorway
| | - Panagiotis Tsiartas
- Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Obstetrics and GynecologyKarolinska InstituteStockholmSweden
- Nordic IVF, Eugin groupSolnaSweden
| | - Ivana Musilova
- Biomedical Research CenterUniversity Hospital Hradec KraloveHradec KraloveCzech Republic
- Department of Obstetrics and GynecologyHospital MostUsti nad LabemCzech Republic
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Alessandri G, Rizzo SM, Mancabelli L, Fontana F, Longhi G, Turroni F, van Sinderen D, Ventura M. Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities. Microb Biotechnol 2024; 17:e14509. [PMID: 38878269 PMCID: PMC11179620 DOI: 10.1111/1751-7915.14509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/18/2024] Open
Abstract
The availability of microbial biobanks for the storage of individual gut microbiota members or their derived and artificially assembled consortia has become fundamental for in vitro investigation of the molecular mechanisms behind microbe-microbe and/or microbe-host interactions. However, to preserve bacterial viability, adequate storage and processing technologies are required. In this study, the effects on cell viability of seven different combinations of cryoprotective agents were evaluated by flow cytometry for 53 bacterial species representing key members of the human gut microbiota after one and 3 months of cryopreservation at -80°C. The obtained results highlighted that no universal cryoprotectant was identified capable of guaranteeing effective recovery of intact cells after cryopreservation for all tested bacteria. However, the presence of inulin or skimmed milk provided high levels of viability protection during cryoexposure. These results were further corroborated by cryopreserving 10 artificial gut microbiota produced through in vitro continuous fermentation system technology. Indeed, in this case, the inclusion of inulin or skimmed milk resulted in a high recovery of viable cells, while also allowing consistent and reliable preservation of the artificial gut microbiota biodiversity. Overall, these results suggest that, although the efficacy of various cryoprotective agents is species-specific, some cryoprotectants based on glycerol and the addition of inulin or skimmed milk are preferable to retain viability and biodiversity for both single bacterial species and artificial gut microbiota.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Aberšek N, Tsiartas P, Soucek O, Andrys C, Musilova I, Jacobsson B, Kacerovsky M. Characterizing of intra-amniotic inflammatory changes associated with chronic inflammation in the placenta marked by elevated amniotic fluid interferon gamma-induced protein 10 (IP-10) in pregnancies complicated by preterm prelabor rupture of membranes. Eur J Obstet Gynecol Reprod Biol 2024; 296:292-298. [PMID: 38503193 DOI: 10.1016/j.ejogrb.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
OBJECTIVES This study aimed to determine the occurrence of intra-amniotic inflammatory changes associated with chronic inflammation in the placenta, marked by elevated levels of interferon gamma-induced protein 10 (IP-10) (≥2200 pg/mL) in the amniotic fluid of women with preterm prelabor rupture of membranes (PPROM). Specifically, the study investigated whether these intra-amniotic inflammatory changes were more common in women with microbial invasion of amniotic cavity (MIAC) and intra-amniotic inflammation (IAI), as indicated by increased amniotic fluid interleukin (IL)-6 concentration (≥3000 pg/mL). STUDY DESIGN A cohort of 114 women with singleton pregnancies complicated by PPROM between 24+0 and 36+6 weeks of gestation were included. Amniotic fluid samples were obtained via amniocentesis upon admission. MIAC diagnosis involved aerobic and anaerobic cultures, as well as polymerase chain reaction (PCR) analysis of the amniotic fluid. Immunoassay tests and enzyme-linked immunosorbent assay (ELISA) were used to determine IL-6 and IP-10 concentrations, respectively. RESULTS Among the participants, 19.3 % and 15.8 % had MIAC and IAI, respectively. The occurrence of intra-amniotic inflammatory changes associated with chronic inflammation in the placenta was similar between women with and without MIAC (25 % vs. 40.9 %, p = 0.136, adjusted p = 0.213). The rate of intra-amniotic inflammatory changes associated with chronic inflammation in the placenta was significantly higher in women with IAI compared to those without, after adjusting for gestational age at sampling (55.6 % vs. 22.9 %, p = 0.005, adjusted p = 0.011). CONCLUSION This study revealed comparable rates of intra-amniotic inflammatory changes associated with chronic inflammation in the placenta in women with and without MIAC, but a higher prevalence of intra-amniotic inflammatory changes associated with chronic inflammation in the placenta in women with IAI. These findings suggest involvement of chronic inflammation even in women with PPROM with acute intra-amniotic inflammation.
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Affiliation(s)
- Nina Aberšek
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Panagiotis Tsiartas
- Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Obstetrics and Gynecology, Karolinska Institute, Stockholm, Sweden; Nordic IVF, Eugin Group, Solna, Sweden
| | - Ondrej Soucek
- Department of Clinical Immunology and Allergy, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ctirad Andrys
- Department of Clinical Immunology and Allergy, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ivana Musilova
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic; Department of Obstetrics and Gynecology, Hospital Most, Krajska zdravotni, a.s., Most, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Genetics and Bioinformatics, Area of Health Data and Digitalization, Institute of Public Health, Oslo, Norway.
| | - Marian Kacerovsky
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic; Department of Obstetrics and Gynecology, Hospital Most, Krajska zdravotni, a.s., Most, Czech Republic
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Ribeiro MC, Levi Y, Moraschini V, Messora MR, Furlaneto FAC. Effects of Prebiotic Therapy on Gastrointestinal Microbiome of Individuals with Different Inflammatory Conditions: A Systematic Review of Randomized Controlled Trials. Probiotics Antimicrob Proteins 2024; 16:673-695. [PMID: 37093515 DOI: 10.1007/s12602-023-10075-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Prebiotics are substrates selectively utilized by host microorganisms conferring a health benefit. The effects of prebiotics on the gut microbiome of individuals with inflammatory processes need further investigations. The purpose of this study was to evaluate the effects of prebiotics on the gastrointestinal microbiome of individuals with some types of inflammatory conditions. Randomized controlled clinical trials (RCTs) evaluating the effects of different prebiotics on the gut microbiome were included. A systematic review of the literature including searches in PubMed/MEDLINE, EMBASE, Cochrane Library, Web of Science, and Scopus databases was performed until 23 March 2023. The risk of bias was assessed using the Cochrane Collaboration's criteria. Qualitative data was tabulated to facilitate comparisons and represented in the form of descriptive statistics and summary tables. Thirty trials, ranging from 12 to 135 patients, were included. The most commonly used prebiotic type was inulin-type fructans, and the treatment duration ranged from 1 to 36 weeks. The majority of the trials investigated the gut microbiome using 16 s rRNA gene sequencing on the Illumina Miseq platform. In general, prebiotic therapy exerted positive effects on inflammatory conditions. An increase in Bifidobacterium genus was the most common shift in bacterial composition observed. Within the limits of this systematic review, it can be suggested that prebiotic therapy presents the potential to favorably modulate the gastrointestinal microbiome of individuals with different types of inflammatory conditions.
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Affiliation(s)
- M C Ribeiro
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil
| | - Ylas Levi
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil
| | - V Moraschini
- Department of Periodontology, Dental Research Division, School of Dentistry, Veiga de Almeida University, Rio de Janeiro, Brazil
| | - M R Messora
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil
| | - F A C Furlaneto
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil.
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Isali I, Helstrom EK, Uzzo N, Lakshmanan A, Nandwana D, Valentine H, Sindhani M, Abbosh P, Bukavina L. Current Trends and Challenges of Microbiome Research in Bladder Cancer. Curr Oncol Rep 2024; 26:292-298. [PMID: 38376627 PMCID: PMC10920447 DOI: 10.1007/s11912-024-01508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2024] [Indexed: 02/21/2024]
Abstract
PURPOSE OF THE REVIEW Microbiome research has provided valuable insights into the associations between microbial communities and bladder cancer. However, this field faces significant challenges that hinder the interpretation, generalization, and translation of findings into clinical practice. This review aims to elucidate these challenges and highlight the importance of addressing them for the advancement of microbiome research in bladder cancer. RECENT FINDINGS Recent findings underscore the complexities involved in microbiome research, particularly in the context of bladder cancer. Challenges include low microbial biomass in urine samples, potential contamination issues during collection and processing, variability in sequencing methods and primer selection, and the difficulty of establishing causality between microbiota and bladder cancer. Studies have shown the impact of sample storage conditions and DNA isolation kits on microbiome analysis, emphasizing the need for standardization. Additionally, variations in urine collection methods can introduce contamination and affect results. The choice of 16S rRNA gene amplicon sequencing or shotgun metagenomic sequencing introduces technical challenges, including primer selection and sequencing read length. Establishing causality between the microbiota and bladder cancer requires experimental methods like fecal microbiota transplantation and human microbiota-associated murine models, which face their own set of challenges. Translating microbiome research into therapeutic applications is hindered by methodological variability, incomplete understanding of bioactive molecules, imperfect animal models, and the inherent heterogeneity of microbiome communities among individuals. Microbiome research in bladder cancer presents significant challenges stemming from technical and conceptual complexities. Addressing these challenges through standardization, improved experimental models, and advanced analytical approaches is essential for advancing our understanding of the microbiome's role in bladder cancer and its potential clinical applications. Achieving this goal can lead to improved patient outcomes and novel therapeutic strategies in the future.
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Affiliation(s)
- Ilaha Isali
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Emma K Helstrom
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Nicole Uzzo
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ankita Lakshmanan
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Devika Nandwana
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Henkel Valentine
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Mohit Sindhani
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Philip Abbosh
- Department of Urology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Laura Bukavina
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
- Case Western Reserve School of Medicine, Cleveland, OH, USA.
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Musilova I, Stranik J, Jacobsson B, Kacerovsky M. Antibiotic treatment reduces the intensity of intraamniotic inflammation in pregnancies with idiopathic vaginal bleeding in the second trimester of pregnancy. Am J Obstet Gynecol 2024; 230:245.e1-245.e14. [PMID: 37516399 DOI: 10.1016/j.ajog.2023.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Idiopathic bleeding in the second trimester of pregnancy complicates <1% of all pregnancies. This pregnancy complication can be caused by alterations in local hemostasis in the decidua due to infection/inflammation in the choriodecidual niche. This condition is associated with intraamniotic inflammatory complications. Antibiotic therapy effectively reduces the intensity of intraamniotic inflammation in certain pregnancy pathologies. However, whether antibiotic administration can reduce the intensity of the intraamniotic inflammatory response or eradicate microorganisms in patients with idiopathic bleeding during the second trimester of pregnancy remains unclear. OBJECTIVE This study primarily aimed to determine whether antimicrobial agents can reduce the magnitude of intraamniotic inflammation in patients with idiopathic bleeding in the second trimester of pregnancy by assessing the concentration of interleukin-6 in the amniotic fluid before and after 7 days of antibiotic treatment. The secondary aim was to determine whether treatment with a combination of antibiotics altered the microbial load of Ureaplasma species DNA in amniotic fluid. STUDY DESIGN This retrospective cohort study included singleton-gestation patients with idiopathic bleeding between 15+0 and 27+6 weeks who underwent transabdominal amniocentesis at the time of admission. Follow-up amniocentesis was performed in a subset of patients unless abortion or delivery occurred earlier. Concentrations of interleukin-6 were measured in the amniotic fluid samples, and the presence of microbial invasion of the amniotic cavity was assessed using culture and molecular microbiological methods. Intraamniotic inflammation was defined as an interleukin-6 concentration ≥3000 pg/mL in the amniotic fluid samples. RESULTS A total of 36 patients with idiopathic bleeding in the second trimester of pregnancy were included. All the patients underwent initial amniocentesis. Patients with intraamniotic inflammation (n=25) were treated using a combination of antibiotics consisting of intravenous ceftriaxone, intravenous metronidazole, and peroral clarithromycin. The patients without intraamniotic inflammation (n=11) were treated expectantly. In total, 25 patients delivered 7 days after admission. All patients with intraamniotic inflammation at the initial amniocentesis who delivered after 7 days underwent follow-up amniocentesis. Treatment with antibiotics decreased the interleukin-6 concentration in the amniotic fluid at follow-up amniocentesis compared with that at the initial amniocentesis in patients with intraamniotic inflammation (median [interquartile range]: 3457 pg/mL [2493-13,203] vs 19,812 pg/mL [11,973-34,518]; P=.0001). Amniotic fluid samples with Ureaplasma species DNA had a lower microbial load at the time of follow-up amniocentesis compared with the initial amniocentesis (median [interquartile range]: 1.5×105 copies DNA/mL [1.3×105-1.7×105] vs 8.0×107 copies DNA/mL [6.7×106-1.6×108]; P=.02). CONCLUSION Antibiotic therapy was associated with reduced intraamniotic inflammation in patients with idiopathic bleeding in the second trimester complicated by intraamniotic inflammation. Moreover, antibiotic treatment has been associated with a reduction in the microbial load of Ureaplasma species DNA in the amniotic fluid.
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Affiliation(s)
- Ivana Musilova
- Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic; Department of Obstetrics and Gynecology, Hospital Most, Krajská zdravotní a.s., Ústí nad Labem, Czech Republic
| | - Jaroslav Stranik
- Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden; Division of Health Data and Digitalisation, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Marian Kacerovsky
- Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic; Department of Obstetrics and Gynecology, Hospital Most, Krajská zdravotní a.s., Ústí nad Labem, Czech Republic.
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11
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Khalid A, Huang Z, Khan IM, Khalid F, Nassar N, Jiang X, Cheng M, Zhan K, Wang Z. Improving broiler health through cecal microbiota transplantation: a comprehensive study on growth, immunity, and microbial diversity. J Anim Sci 2024; 102:skae131. [PMID: 38720654 PMCID: PMC11259951 DOI: 10.1093/jas/skae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/08/2024] [Indexed: 07/21/2024] Open
Abstract
Cecal microbiota has emerged as a prominent intervention target for improving the production and welfare of poultry. This is essential for the overall health and performance of broiler chickens. The current study focused on investigating the effect of cecal microbiota transplantation (CMT) from healthy donor chickens on the growth performance, immunity, and microbial composition of newly hatched chicks and evaluated the effect of sample storage on the microbial diversity of the cecal samples. A healthy "Wannan Yellow Chicken line" was selected as the donor, and 180 1-d-old chicks from the same line were used as recipients for a 60-d feed trial. The chicks were randomly allocated to three groups (60 birds per group) with three replicates in each group. The three treatment groups were CMT-0 (control, normal saline solution), CMT-I (1:12 cecal content, normal saline supplemented with 10% glycerol), and CMT-II (1:6 cecal content, normal saline supplemented with 10% glycerol). The results of weight gain and absolute organ weight showed significant improvements in the CMT-II group compared with the CMT-0 group. Serum IgG level was significantly improved (P < 0.05) in CMT-I compared with that in the CMT-0. However, IL-6 levels increased in CMT-I and then significantly decreased in CMT-II. The cecal microbial diversity of CMT treatment was compared between two groups, fresh samples (FS) and stored samples at-80 °C (SS). The results showed that beneficial taxa, such as Firmicutes and Verrucomicrobiota, were substantially more abundant in both CMT-I and CMT-II than in CMT-0 in both FS and SS. Microbial function analysis at levels 1, 2, and 3 showed improved metabolism, genetic information processing, cellular processes, environmental information processing, and organismal systems in CMT-I and CMT-II for both FS and SS groups. However, the SS group showed decreased microbial diversity and function. To conclude, cecal microbiota transplantation is a promising strategy for enhancing the productivity and health of broiler chickens.
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Affiliation(s)
- Anam Khalid
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
| | - Zhengxuan Huang
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
| | - Ibrar Muhammad Khan
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
| | - Fatima Khalid
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
| | - Nourhan Nassar
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
| | - Xinyu Jiang
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
| | - Maoji Cheng
- Fisugarpeptide Biology Engineering Co. Ltd., Anhui 237000, People’s Republic of China
| | - Kai Zhan
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, 230031 Hefei, Anhui, People’s Republic of China
| | - Zaigui Wang
- College of Life Science, Anhui Agricultural University, 230036, Hefei, Anhui, People’s Republic of China
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12
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Lauko S, Gancarcikova S, Hrckova G, Hajduckova V, Andrejcakova Z, Fecskeova LK, Bertkova I, Hijova E, Kamlarova A, Janicko M, Ambro L, Kvakova M, Gulasova Z, Strojny L, Strkolcova G, Mudronova D, Madar M, Demeckova V, Nemetova D, Pacuta I, Sopkova D. Beneficial Effect of Faecal Microbiota Transplantation on Mild, Moderate and Severe Dextran Sodium Sulphate-Induced Ulcerative Colitis in a Pseudo Germ-Free Animal Model. Biomedicines 2023; 12:43. [PMID: 38255150 PMCID: PMC10813722 DOI: 10.3390/biomedicines12010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Transplantation of faecal microbiota (FMT) is generally considered a safe therapeutic procedure with few adverse effects. The main factors that limit the spread of the use of FMT therapy for idiopathic inflammatory bowel disease (IBD) are the necessity of minimising the risk of infection and transfer of another disease. Obtaining the animal model of UC (ulcerative colitis) by exposure to DSS (dextran sodium sulphate) depends on many factors that significantly affect the result. Per os intake of DSS with water is individual for each animal and results in the development of a range of various forms of induced UC. For this reason, the aim of our study was to evaluate the modulation and regenerative effects of FMT on the clinical and histopathological responses and the changes in the bowel microenvironment in pseudo germ-free (PGF) mice of the BALB/c line subjected to chemical induction of mild, moderate and serious forms of UC. The goal was to obtain new data related to the safety and effectiveness of FMT that can contribute to its improved and optimised use. The animals with mild and moderate forms of UC subjected to FMT treatment exhibited lower severity of the disease and markedly lower damage to the colon, including reduced clinical and histological disease index and decreased inflammatory response of colon mucosa. However, FMT treatment failed to achieve the expected therapeutic effect in animals with the serious form of UC activity. The results of our study indicated a potential safety risk involving development of bacteraemia and also translocation of non-pathogenic representatives of bowel microbiota associated with FMT treatment of animals with a diagnosed serious form of UC.
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Affiliation(s)
- Stanislav Lauko
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Sona Gancarcikova
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Gabriela Hrckova
- Institute of Parasitology, Slovak Academy of Sciences, 041 81 Kosice, Slovakia;
| | - Vanda Hajduckova
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Zuzana Andrejcakova
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (Z.A.); (D.S.)
| | - Livia Kolesar Fecskeova
- Associated Tissue Bank, Faculty of Medicine, Pavol Jozef Safarik University and Louis Pasteur University Hospital (UHLP) in Kosice, 040 11 Kosice, Slovakia;
| | - Izabela Bertkova
- Center of Clinical and Preclinical Research—MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia; (I.B.); (E.H.); (A.K.); (M.K.); (Z.G.); (L.S.)
| | - Emilia Hijova
- Center of Clinical and Preclinical Research—MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia; (I.B.); (E.H.); (A.K.); (M.K.); (Z.G.); (L.S.)
| | - Anna Kamlarova
- Center of Clinical and Preclinical Research—MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia; (I.B.); (E.H.); (A.K.); (M.K.); (Z.G.); (L.S.)
| | - Martin Janicko
- 2nd Department of Internal Medicine, Faculty of Medicine, Pavol Jozef Safarik University and Louis Pasteur University Hospital in Kosice, 040 11 Kosice, Slovakia;
| | - Lubos Ambro
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Safarik University in Kosice, 040 01 Kosice, Slovakia;
| | - Monika Kvakova
- Center of Clinical and Preclinical Research—MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia; (I.B.); (E.H.); (A.K.); (M.K.); (Z.G.); (L.S.)
| | - Zuzana Gulasova
- Center of Clinical and Preclinical Research—MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia; (I.B.); (E.H.); (A.K.); (M.K.); (Z.G.); (L.S.)
| | - Ladislav Strojny
- Center of Clinical and Preclinical Research—MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia; (I.B.); (E.H.); (A.K.); (M.K.); (Z.G.); (L.S.)
| | - Gabriela Strkolcova
- Department of Epizootiology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia;
| | - Dagmar Mudronova
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Marian Madar
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Vlasta Demeckova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, 040 01 Kosice, Slovakia;
| | - Daniela Nemetova
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Ivan Pacuta
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (S.L.); (V.H.); (D.M.); (M.M.); (D.N.); (I.P.)
| | - Drahomira Sopkova
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia; (Z.A.); (D.S.)
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13
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Soucek O, Kacerovsky M, Kacerovska Musilova I, Stranik J, Kukla R, Bolehovska R, Andrys C. Amniotic fluid CD36 in pregnancies complicated by spontaneous preterm delivery: a retrospective cohort study. J Matern Fetal Neonatal Med 2023; 36:2214838. [PMID: 37217453 DOI: 10.1080/14767058.2023.2214838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023]
Abstract
OBJECTIVE The aim of this study was to evaluate CD36 concentrations in amniotic fluid in pregnancies complicated by spontaneous delivery with intact fetal membranes (preterm labor, PTL) and preterm prelabor rupture of membranes (PPROM) with respect to the presence of the intra-amniotic infection. METHODS A total of 80 women with PPROM and 71 with PTL were included in the study. Amniotic fluid samples were obtained by transabdominal amniocentesis. Amniotic fluid CD36 concentrations were assessed by enzyme-linked immunosorbent assay. Microbial colonization of the amniotic cavity (MIAC) was determined by the cultivation and non-cultivation approach. Intra-amniotic inflammation (IAI) was defined as an amniotic fluid bedside interleukin-6 concentration ≥3000 pg/mL. Intra-amniotic infection was characterized by the presence of both MIAC and IAI. RESULTS Women with PPROM with intra-amniotic infection had higher amniotic fluid CD36 concentrations than women without infection (with infection: median 346 pg/mL, IQR 262-384 vs. without infection: median 242 pg/mL, IQR 199-304; p = .006) A positive correlation between amniotic fluid CD36 concentrations and interleukin-6 concentrations was found (rho = 0.48; p < .0001). In PTL pregnancies, no statistically significant difference was found in the amniotic fluid level of CD36 between intra-amniotic infection, sterile IAI, and negative amniotic fluid. CONCLUSIONS The presence of intra-amniotic infection is characterized by higher amniotic fluid CD36 concentrations in pregnancies complicated by PPROM. An amniotic fluid CD36 cutoff value of 252.5 pg/mL was found to be optimal for the prediction of intra-amniotic infection. In PTL pregnancies, no statistically significant change in CD36 concentration was found with respect to the presence of intra-amniotic infection.
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Affiliation(s)
- Ondrej Soucek
- Department of Immunology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Marian Kacerovsky
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ivana Kacerovska Musilova
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jaroslav Stranik
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Rudolf Kukla
- Department of Microbiology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Radka Bolehovska
- Department of Microbiology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ctirad Andrys
- Department of Immunology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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14
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Superdock DK, Zhang W, Poole AC. Processing and storage methods affect oral and gut microbiome composition. Front Microbiol 2023; 14:1253570. [PMID: 37854339 PMCID: PMC10579807 DOI: 10.3389/fmicb.2023.1253570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/08/2023] [Indexed: 10/20/2023] Open
Abstract
In microbiome studies, fecal and oral samples are stored and processed in different ways, which could affect the observed microbiome composition. In this study, we compared storage and processing methods applied to samples prior to DNA extraction to determine how each affected microbial community diversity as assessed by 16S rRNA gene sequencing. We collected dental swabs, saliva, and fecal samples from 10 individuals, with three technical replicates per condition. We assessed four methods of storing and processing fecal samples prior to DNA extraction. We also compared different fractions of thawed saliva and dental samples to fresh samples. We found that lyophilized fecal samples, fresh whole saliva samples, and the supernatant fraction of thawed dental samples had the highest levels of alpha diversity. The supernatant fraction of thawed saliva samples had the second highest evenness compared to fresh saliva samples. Then, we investigated the differences in observed community composition at the domain and phylum levels and identified the amplicon sequence variants (ASVs) that significantly differed in relative abundance between the conditions. Lyophilized fecal samples had a greater prevalence of Archaea as well as a greater ratio of Firmicutes to Bacteroidetes compared to the other conditions. Our results provide practical considerations not only for the selection of storage and processing methods but also for comparing results across studies. Differences in processing and storage methods could be a confounding factor influencing the presence, absence, or differential abundance of microbes reported in conflicting studies.
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Affiliation(s)
| | - Wei Zhang
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Angela C. Poole
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
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15
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Xu L, Kasprzyk-Hordern B. Assessment of the stability of antimicrobials and resistance genes during short- and long-term storage condition: accounting for uncertainties in bioanalytical workflows. Anal Bioanal Chem 2023; 415:6027-6038. [PMID: 37526655 PMCID: PMC10556160 DOI: 10.1007/s00216-023-04874-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/30/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Unravelling complexities in antimicrobial agent-microbe interactions in the context of antimicrobial resistance (AMR) requires robust analytical workflows accounting for all uncertainties. Temporal storage of wastewater samples under refrigerated or frozen conditions prior to chemical and biological analysis is widely used to facilitate laboratory routine but may affect stability of analytes over time. Yet, little knowledge exists regarding stability of biological and chemical determinants in environmental samples, which hampers validity of research outputs. This study examines, for the first time, the stability of 32 antimicrobials (AAs) including commonly used classes of antibiotics and their representative metabolites and variation of 5 antibiotic resistance genes (ARGs) (ermB, sul1, tetW, blaCTX-M, qnrS), as well as intI1 and 16S rRNA genes in a reference wastewater sample stored under freezing condition for up to 1 year. Ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) and quantitative PCR (qPCR) techniques were adopted to measure concentration of AAs and ARGs, respectively. Results suggested that parent compounds are less affected by freezing storage compared to the metabolites. β-Lactams, clindamycin, and N-desmethyl clindamycin are the most-affected compounds which were poorly recovered (34-67%) from the starting concentration. By contrast, sulfonamides, macrolides, quinolones, and azoles are generally stable under freezing condition. No consistent differences were observed in gene copies between fresh and frozen samples, and ermB and tetW showed the highest variabilities at 30% under freezing condition. Overall, this study adds to the current knowledge on environmental AMR monitoring and emphasises the need for standardised protocols for AMR monitoring in the wastewater samples.
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Affiliation(s)
- Like Xu
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Barbara Kasprzyk-Hordern
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Institute for Sustainability, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Water and Innovation Research Centre, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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16
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Cai J, Auster A, Cho S, Lai Z. Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage. J Adv Res 2023; 52:171-201. [PMID: 37419381 PMCID: PMC10555929 DOI: 10.1016/j.jare.2023.07.002] [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: 01/20/2023] [Revised: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND The gut microbiome is a diverse system within the gastrointestinal tract composed of trillions of microorganisms (gut microbiota), along with their genomes. Accumulated evidence has revealed the significance of the gut microbiome in human health and disease. Due to its ability to alter drug/xenobiotic pharmacokinetics and therapeutic outcomes, this once-forgotten "metabolic organ" is receiving increasing attention. In parallel with the growing microbiome-driven studies, traditional analytical techniques and technologies have also evolved, allowing researchers to gain a deeper understanding of the functional and mechanistic effects of gut microbiome. AIM OF REVIEW From a drug development perspective, microbial drug metabolism is becoming increasingly critical as new modalities (e.g., degradation peptides) with potential microbial metabolism implications emerge. The pharmaceutical industry thus has a pressing need to stay up-to-date with, and continue pursuing, research efforts investigating clinical impact of the gut microbiome on drug actions whilst integrating advances in analytical technology and gut microbiome models. Our review aims to practically address this need by comprehensively introducing the latest innovations in microbial drug metabolism research- including strengths and limitations, to aid in mechanistically dissecting the impact of the gut microbiome on drug metabolism and therapeutic impact, and to develop informed strategies to address microbiome-related drug liability and minimize clinical risk. KEY SCIENTIFIC CONCEPTS OF REVIEW We present comprehensive mechanisms and co-contributing factors by which the gut microbiome influences drug therapeutic outcomes. We highlight in vitro, in vivo, and in silico models for elucidating the mechanistic role and clinical impact of the gut microbiome on drugs in combination with high-throughput, functionally oriented, and physiologically relevant techniques. Integrating pharmaceutical knowledge and insight, we provide practical suggestions to pharmaceutical scientists for when, why, how, and what is next in microbial studies for improved drug efficacy and safety, and ultimately, support precision medicine formulation for personalized and efficacious therapies.
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Affiliation(s)
- Jingwei Cai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA.
| | - Alexis Auster
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Sungjoon Cho
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Zijuan Lai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
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17
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Kovaleva A, Poluektova E, Maslennikov R, Karchevskaya A, Shifrin O, Kiryukhin A, Tertychnyy A, Kovalev L, Kovaleva M, Lobanova O, Kudryavtseva A, Krasnov G, Fedorova M, Ivashkin V. Effect of Rebamipide on the Intestinal Barrier, Gut Microbiota Structure and Function, and Symptom Severity Associated with Irritable Bowel Syndrome and Functional Dyspepsia Overlap: A Randomized Controlled Trial. J Clin Med 2023; 12:6064. [PMID: 37763004 PMCID: PMC10531936 DOI: 10.3390/jcm12186064] [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: 07/27/2023] [Revised: 08/30/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Treatment of functional digestive disorders is not always effective. Therefore, a search for new application points for potential drugs is perspective. Our aim is to evaluate the effect of rebamipide on symptom severity, intestinal barrier status, and intestinal microbiota composition and function in patients with diarrheal variant of irritable bowel syndrome overlapping with functional dyspepsia (D-IBSoFD). Sixty patients were randomized to receive trimebutine (TRI group), trimebutine + rebamipide (T + R group), or rebamipide (REB group) for 2 months. At the beginning and end of the study, patients were assessed for general health (SF-36), severity of digestive symptoms (Gastrointestinal Symptom Rating and 7 × 7 scales), state of the intestinal barrier, and composition (16S rRNA gene sequencing) and function (short-chain fatty acid fecal content) of the gut microbiota. The severity of most digestive symptoms was reduced in the REB and T + R groups to levels similar to that observed in the TRI group. The duodenal and sigmoidal lymphocytic and sigmoidal eosinophilic infiltration was decreased only in the REB and T + R groups, not in the TRI group. Serum zonulin levels were significantly decreased only in the REB group. A decrease in intraepithelial lymphocytic infiltration in the duodenum correlated with a decrease in the severity of rumbling and flatulence, while a decrease in infiltration within the sigmoid colon correlated with improved stool consistency and decreased severity of the sensation of incomplete bowel emptying. In conclusion, rebamipide improves the intestinal barrier condition and symptoms in D-IBSoFD. The rebamipide effects are not inferior to those of trimebutine.
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Affiliation(s)
- Aleksandra Kovaleva
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
| | - Elena Poluektova
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- The Scientific Community for Human Microbiome Research, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
| | - Roman Maslennikov
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- The Scientific Community for Human Microbiome Research, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
| | - Anna Karchevskaya
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- Laboratory of General and Clinical Neurophysiology, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 5A Butlerova Str., 117485 Moscow, Russia
- N.N. Burdenko National Medical Research Center of Neurosurgery, 16, 4th Tverskaya-Yamskaya St., 125047 Moscow, Russia
| | - Oleg Shifrin
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
| | - Andrey Kiryukhin
- Endoscopy Unit, The Second University Clinic, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
| | - Aleksandr Tertychnyy
- Institute of Clinical Morphology and Digital Pathology, Sechenov University, Trubetskaya Str., 8, Bld. 2, 119048 Moscow, Russia; (A.T.)
| | - Leonid Kovalev
- Laboratory of Structural Biochemistry of Protein, A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospekt, 33, Bld. 2, 119071 Moscow, Russia
| | - Marina Kovaleva
- Laboratory of Structural Biochemistry of Protein, A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospekt, 33, Bld. 2, 119071 Moscow, Russia
| | - Olga Lobanova
- Institute of Clinical Morphology and Digital Pathology, Sechenov University, Trubetskaya Str., 8, Bld. 2, 119048 Moscow, Russia; (A.T.)
| | - Anna Kudryavtseva
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Bld. 1, 119991 Moscow, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Bld. 1, 119991 Moscow, Russia
| | - Maria Fedorova
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Bld. 1, 119991 Moscow, Russia
| | - Vladimir Ivashkin
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- The Scientific Community for Human Microbiome Research, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
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Hattab J, Marruchella G, Sibra A, Tiscar PG, Todisco G. Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle. Microorganisms 2023; 11:2289. [PMID: 37764133 PMCID: PMC10537324 DOI: 10.3390/microorganisms11092289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.
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Affiliation(s)
- Jasmine Hattab
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
| | - Giuseppe Marruchella
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
| | - Alessandra Sibra
- APHA—Animal & Plant Health Agency, Building 1, Sevington Inland Border Facility, Ashford TN25 6GE, UK;
| | - Pietro Giorgio Tiscar
- Department of Veterinary Medicine, University of Teramo, SP18 Piano d’Accio, 64100 Teramo, Italy; (J.H.); (G.M.)
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Efremova I, Maslennikov R, Poluektova E, Zharkova M, Kudryavtseva A, Krasnov G, Fedorova M, Shirokova E, Kozlov E, Levshina A, Ivashkin V. Gut Dysbiosis and Hemodynamic Changes as Links of the Pathogenesis of Complications of Cirrhosis. Microorganisms 2023; 11:2202. [PMID: 37764046 PMCID: PMC10537778 DOI: 10.3390/microorganisms11092202] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
The aim was to evaluate the relationship between gut dysbiosis and hemodynamic changes (hyperdynamic circulation) in cirrhosis, and between hemodynamic changes and complications of this disease. This study included 47 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Echocardiography with a simultaneous assessment of blood pressure and heart rate was performed to assess systemic hemodynamics. Patients with hyperdynamic circulation had more severe cirrhosis, lower albumin, sodium and prothrombin levels, higher C-reactive protein, aspartate aminotransferase and total bilirubin levels, and higher incidences of portopulmonary hypertension, ascites, overt hepatic encephalopathy, hypoalbuminemia, hypoprothrombinemia, systemic inflammation, and severe hyperbilirubinemia than patients with normodynamic circulation. Patients with hyperdynamic circulation compared with those with normodynamic circulation had increased abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Fusobacteria, Micrococcaceae, Intestinobacter, Clostridium sensu stricto, Proteus and Rumicoccus, and decreased abundance of Bacteroidetes, Bacteroidaceae, Holdemanella, and Butyrivibrio. The systemic vascular resistance and cardiac output values correlated with the abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Micrococcaceae, and Fusobacteria. Heart rate and cardiac output value were negatively correlated with the abundance of Bacteroidetes. The mean pulmonary artery pressure value was positively correlated with the abundance of Proteobacteria and Micrococcaceae, and negatively with the abundance of Holdemanella.
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Affiliation(s)
- Irina Efremova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
| | - Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
- The Interregional Public Organization “Scientific Community for the Promotion of the Clinical Study of the Human Microbiome”, 119991 Moscow, Russia
- Consultative and Diagnostic Center No. 2, Moscow Health Department, 107564 Moscow, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
- The Interregional Public Organization “Scientific Community for the Promotion of the Clinical Study of the Human Microbiome”, 119991 Moscow, Russia
| | - Maria Zharkova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
| | - Anna Kudryavtseva
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia (G.K.); (M.F.)
| | - George Krasnov
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia (G.K.); (M.F.)
| | - Maria Fedorova
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia (G.K.); (M.F.)
| | - Elena Shirokova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
| | - Evgenii Kozlov
- Laboratory of Immunopathology, Department of Clinical Immunology and Allergy, Sechenov University, 119991 Moscow, Russia;
| | - Anna Levshina
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
- Laboratory of Immunopathology, Department of Clinical Immunology and Allergy, Sechenov University, 119991 Moscow, Russia;
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
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Kacerovsky M, Musilova I, Baresova S, Kolarova K, Matulova J, Wiik J, Sengpiel V, Jacobsson B. Cervical excisional treatment increases the risk of intraamniotic infection in subsequent pregnancy complicated by preterm prelabor rupture of membranes. Am J Obstet Gynecol 2023; 229:51.e1-51.e13. [PMID: 36596440 DOI: 10.1016/j.ajog.2022.12.316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/18/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Excisional treatment of cervical intraepithelial neoplasia or very early stages of cervical cancer increases the risk of preterm prelabor rupture of membranes in subsequent pregnancies. The risk increases with the length of the excised cone. The subset of cases with preterm prelabor rupture of membranes and a history of cervical excisional treatment could also be at higher risk of intraamniotic infection/inflammation. However, there is a paucity of relevant information on this subject. OBJECTIVE This study aimed to assess the differences in the rates of intraamniotic infection/inflammation and early-onset neonatal sepsis between singleton preterm prelabor rupture of membranes pregnancies without and with a history of cervical excisional treatment, and to investigate the association between these complications of preterm prelabor rupture of membranes and the excised cone length. STUDY DESIGN This retrospective cohort study included 770 preterm prelabor rupture of membranes pregnancies in which transabdominal amniocentesis was performed as part of standard clinical management to assess the intraamniotic environment. The maternal and perinatal medical records of all included women were reviewed to obtain information on the absence or presence of history of cervical excisional treatment and neonatal outcomes. Women whose records contained any information on history of cervical excisional treatment were contacted by phone and in writing to inform them of the study and request permission to collect relevant information from their medical records. Women were divided into 4 subgroups according to the presence of microorganisms and/or their nucleic acids (through culturing and molecular biology methods) in amniotic fluid and/or intraamniotic inflammation (through amniotic fluid interleukin-6 concentration evaluation): intraamniotic infection (presence of both), sterile intraamniotic inflammation (intraamniotic inflammation alone), microbial invasion of the amniotic cavity without inflammation (presence of microorganisms and/or their nucleic acids in amniotic fluid alone), and negative amniotic fluid for infection/inflammation (absence of both). RESULTS A history of cervical excisional treatment was found in 10% (76/765) of the women. Of these, 82% (62/76) had a history of only 1 treatment, and information on cone length was available for 97% (60/62) of them. Women with a history of cervical excisional treatment had higher rates of intraamniotic infection (with, 25% [19/76] vs without, 12% [85/689]; adjusted odds ratio, 2.5; adjusted P=.004), microbial invasion of the amniotic cavity without inflammation (with, 25% [19/76] vs without, 11% [74/689]; adjusted odds ratio, 3.1; adjusted P<.0001), and early-onset neonatal sepsis (with, 8% [11/76] vs without, 3% [23/689]; adjusted odds ratio, 2.9; adjusted P=.02) compared with those without such history. Quartiles of cone length (range: 3-32 mm) were used to categorize the women into 4 quartile subgroups (first: 3-8 mm; second: 9-12 mm; third: 13-17 mm; and fourth: 18-32 mm). Cone length of ≥18 mm was associated with higher rates of intraamniotic infection (with, 29% [5/15] vs without, 12% [85/689]; adjusted odds ratio, 3.0; adjusted P=.05), microbial invasion of the amniotic cavity without inflammation (with, 40% [6/15] vs without, 11% [74/689]; adjusted odds ratio, 6.1; adjusted P=.003), and early-onset neonatal sepsis (with, 20% [3/15] vs without, 3% [23/689]; adjusted odds ratio, 5.7; adjusted P=.02). CONCLUSION History of cervical excisional treatment increases risks of intraamniotic infection, microbial invasion of the amniotic cavity without inflammation, and development of early-onset neonatal sepsis in a subsequent pregnancy complicated by preterm prelabor rupture of membranes.
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Affiliation(s)
- Marian Kacerovsky
- Department of Obstetrics and Gynecology, University Hospital Hradec Králové Charles University, Faculty of Medicine in Hradec Králové, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic.
| | - Ivana Musilova
- Department of Obstetrics and Gynecology, University Hospital Hradec Králové Charles University, Faculty of Medicine in Hradec Králové, Hradec Králové, Czech Republic
| | - Simona Baresova
- Department of Obstetrics and Gynecology, University Hospital Hradec Králové Charles University, Faculty of Medicine in Hradec Králové, Hradec Králové, Czech Republic
| | - Klara Kolarova
- Department of Obstetrics and Gynecology, University Hospital Hradec Králové Charles University, Faculty of Medicine in Hradec Králové, Hradec Králové, Czech Republic
| | - Jana Matulova
- Department of Non-Medical Studies, Charles University, Faculty of Medicine in Hradec Králové, Hradec Králové, Czech Republic
| | - Johanna Wiik
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Verena Sengpiel
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
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Li XM, Shi X, Yao Y, Shen YC, Wu XL, Cai T, Liang LX, Wang F. Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis. Microbiol Spectr 2023; 11:e0429722. [PMID: 37093040 PMCID: PMC10269478 DOI: 10.1128/spectrum.04297-22] [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: 10/21/2022] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using stool sample preservation experiments for up to 1 year. The stool samples from feces of healthy volunteers were grouped based on whether absolute ethanol was added and whether they were hypothermically preserved. Besides, we performed a systematic review to combine current fecal microbiota preservation evidence. We found that Proteobacteria changed significantly and Veillonellaceae decreased significantly in the 12th month in the room temperature + absolute ethanol group. The four cryopreservation groups have more similarities with fresh sample in the 12 months; however, different cryopreservation methods have different effects on several phyla, families, and genera. A systematic review showed that the Shannon diversity and Simpson index of samples stored in RNAlater for 1 month were not statistically significant compared with those stored immediately at -80°C (P = 0.220 and P = 0.123, respectively). The -80°C refrigerator and liquid nitrogen cryopreservation with 10% glycerine can both maintain stable microbiota of stool samples for long-term preservation. The addition of absolute ethanol to cryopreserved samples had no significant difference in the effect of preserving fecal microbial characteristics. Our study provides empirical insights into preservation details for future studies of the long-term preservation of fecal microbiota. Systematic review and meta-analysis found that the gut microbiota structure, composition, and diversity of samples preserved by storage methods, such as preservation solution, are relatively stable, which were suitable for short-term storage at room temperature. IMPORTANCE The study of gut bacteria has become increasingly popular, and fecal sample preservation methods and times need to be standardized. Here, we detail a 12-month study of fecal sample preservation, and our study provides an empirical reference about experimental details for long-term high-quality storage of fecal samples in the field of gut microbiology research. The results showed that the combination of -80°C/liquid nitrogen deep cryopreservation and 10% glycerol was the most effective method for the preservation of stool samples, which is suitable for long-term storage for at least 12 months. The addition of anhydrous ethanol to the deep cryopreserved samples did not make a significant difference in the preservation of fecal microbiological characteristics. Combined with the results of systematic reviews and meta-analyses, we believe that, when researchers preserve fecal specimens, it is essential to select the proper preservation method and time period in accordance with the goal of the study.
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Affiliation(s)
- Xin-meng Li
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiao Shi
- Department of Dermatology, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yao Yao
- Department of Gastroenterology, Zhangjiajie People’s Hospital, Zhangjiajie, Hunan, China
| | - Yi-cun Shen
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiang-ling Wu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Ting Cai
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Lun-xi Liang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Fen Wang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
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Suzuki-Hashido N, Tsuchida S, Azumano A, Goossens B, Saldivar DAR, Stark DJ, Tuuga A, Ushida K, Matsuda I. Isolation of Bacteria from Freeze-Dried Samples and the Functional Characterization of Species-Specific Lactic Acid Bacteria with a Comparison of Wild and Captive Proboscis Monkeys. Microorganisms 2023; 11:1458. [PMID: 37374963 DOI: 10.3390/microorganisms11061458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Previously, we isolated a novel lactic acid bacteria species (Lactobacillus nasalidis) from the fresh forestomach contents of a captive proboscis monkey (Nasalis larvatus) in a Japanese zoo. In this study, we isolated two strains of L. nasalidis from the freeze-dried forestomach contents of a wild proboscis monkey inhabiting a riverine forest in Malaysia. The samples had been stored for more than six years. Phenotypic analysis showed that strains isolated from the wild individual had more diverse sugar utilization and lower salt tolerance than strains previously isolated from the captive counterpart. These phenotypic differences are most likely induced by feeding conditions; wild individuals consume a wide variety of natural food, unlike their zoo-raised counterparts that consume formula feed with sodium sufficiency. Since 16s rRNA sequences of L. nasalidis were detected in the previously created 16S rRNA libraries of wild, provisioned, and captive proboscis monkeys in Malaysia and Japan, L. nasalidis may be an essential bacterium of the foregut microbial community of the proboscis monkey. The currently established method for the isolation of gut bacteria from freeze-dried samples under storage will be applicable to many already-stored precious samples.
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Affiliation(s)
- Nami Suzuki-Hashido
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku 102-0083, Tokyo, Japan
| | - Sayaka Tsuchida
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | | | - Benoit Goossens
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Diana A Ramirez Saldivar
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Danica J Stark
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Kazunari Ushida
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | - Ikki Matsuda
- Wildlife Research Center, Kyoto University, Sakyo-ku 606-8203, Kyoto, Japan
- Academy of Emerging Sciences, Chubu University, Kasugai 487-8501, Aichi, Japan
- Chubu Institute for Advanced Studies, Chubu University, Kasugai 487-8501, Aichi, Japan
- Institute for Tropical Biology and Conservation, University Malaysia Sabah, Kota Kinabalu 88100, Malaysia
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23
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Kool J, Tymchenko L, Shetty SA, Fuentes S. Reducing bias in microbiome research: Comparing methods from sample collection to sequencing. Front Microbiol 2023; 14:1094800. [PMID: 37065158 PMCID: PMC10101209 DOI: 10.3389/fmicb.2023.1094800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/22/2023] [Indexed: 04/01/2023] Open
Abstract
BackgroundMicrobiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples.MethodsHuman fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene·GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls.ResultsSamples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs.ConclusionOur study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.
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Affiliation(s)
- Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Liza Tymchenko
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sudarshan A. Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- *Correspondence: Susana Fuentes
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Burnham CM, McKenney EA, Heugten KA, Minter LJ, Trivedi S. Effect of fecal preservation method on captive southern white rhinoceros gut microbiome. WILDLIFE SOC B 2023. [DOI: 10.1002/wsb.1436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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25
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Ivashkin V, Shifrin O, Maslennikov R, Poluektova E, Korolev A, Kudryavtseva A, Krasnov G, Benuni N, Barbara G. Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study. BMC Gastroenterol 2023; 23:82. [PMID: 36959568 PMCID: PMC10037807 DOI: 10.1186/s12876-023-02690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Rifaximin effectively treats symptomatic uncomplicated diverticular disease (SUDD) and has shown eubiotic potential (i.e., an increase in resident microbial elements with potential beneficial effects) in other diseases. This study investigated changes in the fecal microbiome of patients with SUDD after repeated monthly treatment with rifaximin and the association of these changes with the severity of abdominal pain. METHODS This was a single-center, prospective, observational, uncontrolled cohort study. Patients received rifaximin 400 mg twice a day for 7 days per month for 6 months. Abdominal pain (assessed on a 4-point scale from 0 [no pain] to 3 [severe pain]) and fecal microbiome (assessed using 16 S rRNA gene sequencing) were assessed at inclusion (baseline) and 3 and 6 months. The Spearman's rank test analyzed the relationship between changes in the gut microbiome and the severity of abdominal pain. A p-value ≤ 0.05 was considered statistically significant. RESULTS Of the 23 patients enrolled, 12 patients completed the study and were included in the analysis. Baseline abdominal pain levels decreased significantly after 3 (p = 0.036) and 6 (p = 0.008) months of treatment with rifaximin. The abundance of Akkermansia in the fecal microbiome was significantly higher at 3 (p = 0.017) and 6 (p = 0.015) months versus baseline. The abundance of Ruminococcaceae (p = 0.034), Veillonellaceae (p = 0.028), and Dialister (p = 0.036) were significantly increased at 6 months versus baseline, whereas Anaerostipes (p = 0.049) was significantly decreased. The severity of abdominal pain was negatively correlated with the abundance of Akkermansia (r=-0.482; p = 0.003) and Ruminococcaceae (r=-0.371; p = 0.026) but not with Veillonellaceae, Dialister, or Anaerostipes. After 3 months of rifaximin, abdominal pain was significantly less in patients with Akkermansia in their fecal microbiome than in patients without Akkermansia (p = 0.022). CONCLUSION The eubiotic effect of rifaximin was associated with decreased abdominal pain in patients with SUDD.
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Affiliation(s)
- Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
- Scientific Community for the Human Microbiome Research, Moscow, Russian Federation
| | - Oleg Shifrin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
| | - Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation.
- Scientific Community for the Human Microbiome Research, Moscow, Russian Federation.
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
- Scientific Community for the Human Microbiome Research, Moscow, Russian Federation
| | - Alexander Korolev
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
| | - Anna Kudryavtseva
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nona Benuni
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences, University of Bologna, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy
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Zouiouich S, Byrd DA, Hua X, Karwa S, Wan Y, Shi J, Humphrey GC, Ackermann GL, Knight R, Abnet CC, Vogtmann E, Sinha R. Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods. Cancer Epidemiol Biomarkers Prev 2023; 32:444-451. [PMID: 36649143 PMCID: PMC10498478 DOI: 10.1158/1055-9965.epi-22-0883] [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: 08/12/2022] [Revised: 11/18/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. We investigated the impact of sample storage at -80°C for 2 years on the stability of the V4 region of the 16S rRNA gene across seven different collection methods (i.e., no additive, 95% ethanol, RNAlater stabilization solution, fecal occult blood test cards, and fecal immunochemical test tubes for feces; OMNIgene ORAL tubes and Scope mouthwash for saliva) among 51 healthy volunteers. METHODS Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the 20 most abundant genera, three alpha-diversity metrics, and the first principal coordinates of three beta-diversity matrices. RESULTS The subject variability was much higher than the variability introduced by the sample collection type, and storage time. For fecal samples, microbial stability over 2 years was high across collection methods (range, ICCs = 0.70-0.99), except for the samples collected with no additive (range, ICCs = 0.23-0.83). For oral samples, most microbiome diversity measures were stable over time with ICCs above 0.74; however, ICCs for the samples collected with Scope mouthwash were lower for two alpha-diversity measures, Faith's phylogenetic diversity (0.23) and the observed number of operational taxonomic units (0.23). CONCLUSIONS Fecal and oral samples in most used collection methods are stable for microbiome analyses after 2 years at -80°C, except for fecal samples with no additive. IMPACT This study provides evidence that samples stored for an extended period from prospective studies are useful for microbiome analyses.
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Affiliation(s)
- Semi Zouiouich
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Doratha A Byrd
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xing Hua
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Smriti Karwa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Gregory C Humphrey
- Department of Pediatrics, University of California, San Diego, California
| | - Gail L Ackermann
- Department of Pediatrics, University of California, San Diego, California
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, California
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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Carbia C, Bastiaanssen TFS, Iannone LF, García-Cabrerizo R, Boscaini S, Berding K, Strain CR, Clarke G, Stanton C, Dinan TG, Cryan JF. The Microbiome-Gut-Brain axis regulates social cognition & craving in young binge drinkers. EBioMedicine 2023; 89:104442. [PMID: 36739238 PMCID: PMC10025767 DOI: 10.1016/j.ebiom.2023.104442] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Binge drinking is the consumption of an excessive amount of alcohol in a short period of time. This pattern of consumption is highly prevalent during the crucial developmental period of adolescence. Recently, the severity of alcohol use disorders (AUDs) has been linked with microbiome alterations suggesting a role for the gut microbiome in its development. Furthermore, a strong link has emerged too between microbiome composition and socio-emotional functioning across different disorders including AUD. The aim of this study was to investigate the potential link (and its predictive value) between alcohol-related altered microbial profile, social cognition, impulsivity and craving. METHODS Young people (N = 71) aged 18-25 reported their alcohol use and underwent a neuropsychological evaluation. Craving was measured at baseline and three months later. Diet was controlled for. Blood, saliva and hair samples were taken for inflammatory, kynurenine and cortisol analysis. Stool samples were provided for shotgun metagenomic sequencing and short-chain fatty acids (SCFAs) were measured. FINDINGS Binge drinking was associated with distinct microbiome alterations and emotional recognition difficulties. Associations were found for several microbiome species with emotional processing and impulsivity. Craving showed a strong link with alterations in microbiome composition and neuroactive potential over time. INTERPRETATION In conclusion, this research demonstrates alterations in the gut microbiome of young binge drinkers (BDs) and identifies early biomarkers of craving. Associations between emotional processing and microbiome composition further support the growing literature on the gut microbiome as a regulator of social cognition. These findings are of relevance for new gut-derived interventions directed at improving early alcohol-related alterations during the vulnerability period of adolescence. FUNDING C.C. and R.G-C. received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754535. APC Microbiome Ireland is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan [grant no. SFI/12/RC/2273_P2]. J.F.C has research support from Cremo, Pharmavite, DuPont and Nutricia. He has spoken at meetings sponsored by food and pharmaceutical companies. G.C. has received honoraria from Janssen, Probi, and Apsen as an invited speaker; is in receipt of research funding from Pharmavite, Fonterra, Nestle and Reckitt; and is a paid consultant for Yakult, Zentiva and Heel pharmaceuticals. All the authors declare no competing interests.
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Affiliation(s)
- Carina Carbia
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | | | | | | | - Serena Boscaini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Kirsten Berding
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | | | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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Loublier C, Taminiau B, Heinen J, Lecoq L, Amory H, Daube G, Cesarini C. Evaluation of Bacterial Composition and Viability of Equine Feces after Processing for Transplantation. Microorganisms 2023; 11:microorganisms11020231. [PMID: 36838196 PMCID: PMC9966902 DOI: 10.3390/microorganisms11020231] [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: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has been used empirically for decades in equine medicine to treat intestinal dysbiosis but evidence-based information is scarce. This in vitro study aimed at assessing the effect of a commonly used pre-FMT processing method on the bacterial composition and viability of the fecal filtrate. Three samples of fresh equine manure (T0) were processed identically: the initial manure was mixed with 1 L of lukewarm water and chopped using an immersion blender to obtain a mixture (T1), which was left uncovered during 30 min (T2) and percolated through a sieve to obtain a fecal filtrate (T3). Samples were taken throughout the procedure (Tn) and immediately stored at 4 °C until processing. The 16S rDNA amplicon profiling associated with propidium monoazide treatment was performed on each sample to select live bacteria. Analyses of α and β diversity and main bacterial populations and quantitative (qPCR) analysis were performed and statistically compared (significance p < 0.05) between time points (T0-T3). No significant differences in ecological indices or mean estimated total living bacteria were found in the final fecal filtrate (T3) in regard to the original manure (T0); however, relative abundances of some minor genera (Fibrobacter, WCHB1-41_ge and Akkermansia) were significantly different in the final filtrate. In conclusion, the results support the viability of the major bacterial populations in equine feces when using the described pre-FMT protocol.
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Affiliation(s)
- Clémence Loublier
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Department of Food Sciences—Microbiology, Faculty of Veterinary Medicine, University of Liege, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Julia Heinen
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Laureline Lecoq
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Hélène Amory
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Department of Food Sciences—Microbiology, Faculty of Veterinary Medicine, University of Liege, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Carla Cesarini
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Correspondence:
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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Results of a Clinical Trial Showing Changes to the Faecal Microbiome in Racing Thoroughbreds after Feeding a Nutritional Supplement. Vet Sci 2022; 10:vetsci10010027. [PMID: 36669028 PMCID: PMC9861731 DOI: 10.3390/vetsci10010027] [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: 10/23/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing (NGS) has been used to evaluate the effect of various interventions on the equine microbiome. The aim of this randomised blinded clinical trial was to determine if a prebiotic nutritional supplement would result in a change from baseline in the faecal microbiome composition of racing Thoroughbred horses in training being fed a high concentrate/grain-based diet to be more similar to that found in forage fed/pasture grazed horses. Thirty-two horses on one training yard were randomised to either receive the supplement or not. Faecal samples were collected at baseline, 6 and 12 weeks for NGS of the 16S ribosomal subunit gene. Twenty-two horses completed the trial, met the inclusion criteria and were included in the intention to treat analysis; 20 horses were included in the per protocol analysis. The mean and median percent decreases in Bacteroidetes, increases in Firmicutes and the Firmicutes:Bacteroidetes ratio were significantly greater than zero for the treated horses only. Supplemented horses (8/10) were more likely than control horses (2/10) to show an increase in Firmicutes of a ≥9% with ≥24% increase in Clostridia, ≥5% decrease in Bacteroidetes, ≥16% increase in the F:B ratio and ≥2% increase in Actinobacteria (RR = 4, 95% CI: 1.1-14.4, p = 0.01). This provides useful information for further investigations on long-term effects on the microbiome and on health and racing-related outcomes.
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31
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Yun HS, Lee JH, Choo YS, Pak JH, Kim HS, Kim YS, Yoon HS. Environmental Factors Associated with the Eukaryotic Microbial Diversity of Ulleungdo Volcanic Island in South Korea. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261721100568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Love CJ, Gubert C, Kodikara S, Kong G, Lê Cao KA, Hannan AJ. Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples. STAR Protoc 2022; 3:101772. [PMID: 36313541 PMCID: PMC9597187 DOI: 10.1016/j.xpro.2022.101772] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to profile gut bacterial populations using rodent fecal samples. We describe the optimal procedures for collecting rodent fecal samples, isolating genomic DNA, 16S rRNA gene V4 region sequencing, and bioinformatic analyses. This protocol includes detailed instructions and example outputs to ensure accurate, reproducible results and data visualization. Comprehensive troubleshooting and limitation sections address technical and statistical issues that may arise when profiling microbiota. For complete details on the use and execution of this protocol, please refer to Gubert et al. (2022).
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Affiliation(s)
- Chloe J. Love
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Carolina Gubert
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia,Corresponding author
| | - Saritha Kodikara
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia,Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Parkville VIC, 3010, Australia
| | - Geraldine Kong
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kim-Anh Lê Cao
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Anthony J. Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia,Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia,Corresponding author
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Siddiqui NZ, Rehman AU, Yousuf W, khan AI, Farooqui NA, Zang S, Xin Y, Wang L. Effect of crude polysaccharide from seaweed, Dictyopteris divaricata (CDDP) on gut microbiota restoration and anti-diabetic activity in streptozotocin (STZ)-induced T1DM mice. Gut Pathog 2022; 14:39. [PMID: 36115959 PMCID: PMC9482207 DOI: 10.1186/s13099-022-00512-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/01/2022] [Indexed: 11/10/2022] Open
Abstract
Type-1 Diabetes Mellitus (T1DM) is regarded as a multifunctional, immune-related disease which causes massive destruction of islet β-cells in pancreas resulting in hyperglycemic, hypoinsulinemia and hyperlipidimic conditions. The aim of the present study, was to investigate the hypothesis that streptozotocin (STZ)-induced T1DM in Balb/c mice when treated with crude polysaccharide from seaweed, Dictyopteris divaricata (CDDP) depicts improvement in diabetes-related symptoms. Treatment with CDDP resulted in decreased body weight loss, improved food consumption and water intake disbalances. The CDDP effectively improved fasting blood glucose, oral glucose tolerance (OGTT), serum insulin, insulin secretion, rejuvenation of β-cells mass, serum lipid profile and pro-inflammatory cytokines levels. Additionally, treatment with CDDP increased the population of beneficial bacteria such as Firmicutes, Bacteroidetes and Lactobacillus at phylum, family and genus levels by 16S rRNA sequencing. Furthermore, immunohistological examination confirmed that CDDP reduces the inflammation and restored the structural morphology of colon and upraised the levels of insulin receptor substrate-1 (IRS-1), Mucin-2 (MUC-2) and tight-junction proteins (TJs) whereby maintaining the gut structures and barrier permeability. Thus, the above presented data, highlights the safe and therapeutic effects of crude polysaccharide (CDDP) from D. divaricata in the treatment and restoration of T1DM disorders and can be used as a food supplement alternative to diabetes medicine.
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Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods. PLoS One 2022; 17:e0267992. [PMID: 36107863 PMCID: PMC9477292 DOI: 10.1371/journal.pone.0267992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine bulk milk, we assembled and tested a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. The following protocol variations were examined:: BCMC enumeration (colony enumeration or microscopy), sample volume (200 μl to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was more accurate for quantification of the BCMC contents. We found that least 10 mL (≥ 104 cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. Cell lysis procedures conferred the greatest changes to milk microbiota composition and these effects were confirmed to provide similar results for commercial milk samples. Overall, our systematic approach with the BCMC is broadly applicable to other milk, food, and environmental samples therefore recommended for improving accuracy of culture-independent, DNA sequence-based analyses of microbial composition in different habitats.
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Cryopreservation of stool samples altered the microbial viability quantitively and compositionally. Arch Microbiol 2022; 204:557. [PMID: 35972563 DOI: 10.1007/s00203-022-03169-1] [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: 10/31/2021] [Revised: 05/24/2022] [Accepted: 08/04/2022] [Indexed: 11/02/2022]
Abstract
Stool is the most commonly used sample for gut microbiota analysis in humans and animals. Cryopreservation of stool at - 80 °C is a feasible and simple method in clinics and researches, especially in large-scale cohort studies. However, the viability of bacteria in stool after freezing has yet well-demonstrated quantitatively and compositionally. This study determined the viable microbiota of samples under cryopreservation at - 80 °C, relative to fresh samples and that stored at ambient. Stool samples were collected from three healthy adults. Propidium monoazide treatment combined with quantitative PCR and 16S rRNA gene sequencing was performed to target viable microbiota. After freezing, the number of viable bacteria decreased, though inter-individual difference existed. Notably, the alpha diversity of viable microbiota after freezing did not change significantly, while its composition changed. Freezing significantly reduced the viable bacteria in Gram-negative genera of Bacteroidetes and Firmicutes, and proportionally increased Gram-positive bacteria in genera of Actinobacteria and Firmicutes, including Bifidobacterium, Collinsella and Blautia, implying that the cell envelope structure associated with the bacterial sensitivity to freezing. On the contrary, the room temperature storage not only decreased the number of viable bacteria, but also decreased the microbial alpha diversity, and remarkably enriched facultative anaerobes of Escherichia-Shigella, Enterococcus and Lactococcus, some of which are opportunistic pathogens. Our findings suggested that changes in viable microbiota in stool samples caused by cryopreservation should be paid enough attention for downstream utilization.
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Liu C, Lei J, Zhang M, Wu F, Ren M, Yang J, Wu Q, Shi X. Optimization of Preservation Methods Provides Insights into Photosynthetic Picoeukaryotes in Lakes. Microbiol Spectr 2022; 10:e0255721. [PMID: 35546573 PMCID: PMC9241741 DOI: 10.1128/spectrum.02557-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/18/2022] [Indexed: 11/28/2022] Open
Abstract
As the key contributor to plankton biomass and nutrient cycling in aquatic ecosystems, photosynthetic picoeukaryotes (PPEs) have been recently investigated in freshwater ecosystems. However, the limited access to remote areas creates challenges for PPE sample preservation before sorting and counting by flow cytometry (FCM) in the laboratory. Here, we explored the effects of different preservation methods on the PPE community by combining FCM sorting and high-throughput sequencing. Our results showed that dimethyl sulfoxide (DMSO) cryoprotection could destroy the fluorescence and cell structure of the PPEs, making the subsequent FCM analysis and sorting difficult. Aldehyde fixation maintained the PPE fluorescence, and the fixed samples were of sufficient quality for abundance analysis and sorting by FCM. However, the sequencing results showed that, after preservation by aldehydes, the proportion of PPEs dramatically decreased to approximately 10%, in comparison to 90% in the fresh samples, and the sequences of Ascomycota significantly increased. In contrast, preservation with Pluronic F68 (F68) not only could maintain the PPE abundance close to the initial value but also could keep the PPE community similar to that in the fresh samples over a storage time of 6 months. Thus, F68 cryopreservation is a suitable preservation method for PPE communities from freshwater lakes. IMPORTANCE PPEs contribute significantly to primary productivity in freshwater ecosystems. The combination of FCM sorting and high-throughput sequencing has been shown to be a powerful approach and can largely improve our view of the PPE diversity. However, the water samples could not be counted and sorted immediately after sampling from many lakes due to the inaccessibility of FCM in the field. Thus, the comparison of different preservation methods that allow subsequent analysis of the community structure by high-throughput sequencing is an urgent need. Our results indicated that F68 cryopreservation could maintain the PPE abundance close to the initial value and keep the community similar to that in the fresh samples over a storage time of 6 months.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Lei
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinsheng Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaiyin, China
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Maslennikov R, Ivashkin V, Alieva A, Poluektova E, Kudryavtseva A, Krasnov G, Zharkova M, Zharikov Y. Gut dysbiosis and body composition in cirrhosis. World J Hepatol 2022; 14:1210-1225. [PMID: 35978666 PMCID: PMC9258262 DOI: 10.4254/wjh.v14.i6.1210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/09/2021] [Accepted: 05/14/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut dysbiosis and changes in body composition (i.e., a decrease in the proportion of muscle mass and an increase in extracellular fluid) are common in cirrhosis.
AIM To study the relationship between the gut microbiota and body composition in cirrhosis.
METHODS This observational study included 46 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Multifrequency bioelectrical impedance analysis was performed to assess body composition in these patients.
RESULTS An increase in fat mass and a decrease in body cell mass were noted in 23/46 (50.0%) and 15/46 (32.6%) patients, respectively. Changes in the gut microbiome were not independently associated with the fat mass percentage in cirrhosis. The abundance of Bacteroidaceae (P = 0.041) and Eggerthella (P = 0.001) increased, whereas that of Erysipelatoclostridiaceae (P = 0.006), Catenibacterium (P = 0.021), Coprococcus (P = 0.033), Desulfovibrio (P = 0.043), Intestinimonas (P = 0.028), and Senegalimassilia (P = 0.015) decreased in the gut microbiome of patients with body cell mass deficiency. The amount of extracellular fluid increased in 22/46 (47.6%) patients. Proteobacteria abundance (P < 0.001) increased, whereas Firmicutes (P = 0.023), Actinobacteria (P = 0.026), Bacilli (P = 0.008), Anaerovoraceceae (P = 0.027), Christensenellaceae (P = 0.038), Eggerthellaceae (P = 0.047), Erysipelatoclostridiaceae (P = 0.015), Erysipelotrichaceae (P = 0.003), Oscillospiraceae (P = 0.024), Rikenellaceae (P = 0.002), Collinsella (P = 0.030), Hungatella (P = 0.040), Peptococcaceae (P = 0.023), Slackia (P = 0.008), and Senegalimassilia (P = 0.024) abundance decreased in these patients. Patients with clinically significant ascites (n = 9) had a higher abundance of Proteobacteria (P = 0.031) and a lower abundance of Actinobacteria (P = 0.019) and Bacteroidetes (P = 0.046) than patients without clinically significant ascites (n = 37).
CONCLUSION Changes in the amount of body cell mass and extracellular fluid are associated with changes in the gut microbiome in cirrhosis patients.
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Affiliation(s)
- Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Department of Internal Medicine, Сonsultative and Diagnostic Center No. 2, Moscow City Health Department, Moscow 107564, Russia
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Aliya Alieva
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Anna Kudryavtseva
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George Krasnov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Zharkova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Yuri Zharikov
- Department of Anatomy, Sechenov University, Moscow 119435, Russia
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Hua H, Meydan C, Afshin EE, Lili LN, D’Adamo CR, Rickard N, Dudley JT, Price ND, Zhang B, Mason CE. A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling. Front Immunol 2022; 13:889702. [PMID: 35711426 PMCID: PMC9196042 DOI: 10.3389/fimmu.2022.889702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.
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Affiliation(s)
- Hui Hua
- Thorne HealthTech, New York, NY, United States
| | - Cem Meydan
- Thorne HealthTech, New York, NY, United States
| | | | | | - Christopher R. D’Adamo
- Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | | | - Nathan D. Price
- Thorne HealthTech, New York, NY, United States
- Institute for Systems Biology, Seattle, WA, United States
| | - Bodi Zhang
- Thorne HealthTech, New York, NY, United States
| | - Christopher E. Mason
- Thorne HealthTech, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, United States
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Huang R, Wu F, Zhou Q, Wei W, Yue J, Xiao B, Luo Z. Lactobacillus and intestinal diseases: mechanisms of action and clinical applications. Microbiol Res 2022; 260:127019. [DOI: 10.1016/j.micres.2022.127019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
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Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest 2022; 132:e154944. [PMID: 35362479 PMCID: PMC8970668 DOI: 10.1172/jci154944] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.
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Affiliation(s)
| | - Jennifer L. Pluznick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven L. Salzberg
- Department of Biomedical Engineering
- Department of Computer Science, and
- Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Cynthia L. Sears
- Department of Medicine and
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Jones CB, White JR, Ernst SE, Sfanos KS, Peiffer LB. Incorporation of Data From Multiple Hypervariable Regions when Analyzing Bacterial 16S rRNA Gene Sequencing Data. Front Genet 2022; 13:799615. [PMID: 35432480 PMCID: PMC9009396 DOI: 10.3389/fgene.2022.799615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/08/2022] [Indexed: 01/04/2023] Open
Abstract
Short read 16 S rRNA amplicon sequencing is a common technique used in microbiome research. However, inaccuracies in estimated bacterial community composition can occur due to amplification bias of the targeted hypervariable region. A potential solution is to sequence and assess multiple hypervariable regions in tandem, yet there is currently no consensus as to the appropriate method for analyzing this data. Additionally, there are many sequence analysis resources for data produced from the Illumina platform, but fewer open-source options available for data from the Ion Torrent platform. Herein, we present an analysis pipeline using open-source analysis platforms that integrates data from multiple hypervariable regions and is compatible with data produced from the Ion Torrent platform. We used the ThermoFisher Ion 16 S Metagenomics Kit and a mock community of twenty bacterial strains to assess taxonomic classification of six amplicons from separate hypervariable regions (V2, V3, V4, V6-7, V8, V9) using our analysis pipeline. We report that different amplicons have different specificities for taxonomic classification, which also has implications for global level analyses such as alpha and beta diversity. Finally, we utilize a generalized linear modeling approach to statistically integrate the results from multiple hypervariable regions and apply this methodology to data from a representative clinical cohort. We conclude that examining sequencing results across multiple hypervariable regions provides more taxonomic information than sequencing across a single region. The data across multiple hypervariable regions can be combined using generalized linear models to enhance the statistical evaluation of overall differences in community structure and relatedness among sample groups.
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Affiliation(s)
- Carli B. Jones
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Sarah E. Ernst
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Karen S. Sfanos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Deparment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Lauren B. Peiffer, ; Karen S. Sfanos,
| | - Lauren B. Peiffer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Lauren B. Peiffer, ; Karen S. Sfanos,
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Kacerovsky M, Stranik J, Matulova J, Chalupska M, Mls J, Faist T, Hornychova H, Kukla R, Bolehovska R, Bostik P, Jacobsson B, Musilova I. Clinical characteristics of colonization of the amniotic cavity in women with preterm prelabor rupture of membranes, a retrospective study. Sci Rep 2022; 12:5062. [PMID: 35332204 PMCID: PMC8948248 DOI: 10.1038/s41598-022-09042-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/09/2022] [Indexed: 12/16/2022] Open
Abstract
To determine the main clinical characteristics of preterm prelabor rupture of membranes (PPROM) complicated by colonization of the amniotic cavity (microbial invasion of the amniotic cavity without intra-amniotic inflammation). A total of 302 women with PPROM were included. Transabdominal amniocentesis was performed and amniotic fluid was assessed. Based of microbial invasion of the amniotic cavity and intra-amniotic inflammation (interleukin-6 ≥ 3000 pg/mL), the women were divided into following groups: intra-amniotic infection, sterile intra-amniotic inflammation, colonization of the amniotic cavity, and negative amniotic fluid. Colonization was found in 11% (32/302) of the women. The most common bacteria identified in the amniotic fluid were Ureaplasma spp. with a lower burden than those with intra-amniotic infection (p = 0.03). The intensity of intra-amniotic inflammatory response measured by interleukin-6 was higher in women with colonization than in those with negative amniotic fluid (medians: 961 pg/mL vs. 616 pg/mL; p = 0.04). Women with colonization had higher rates of acute inflammatory placental lesions than those with negative amniotic fluid. In PPROM, colonization, caused mainly by microorganisms from the lower genital tract, might represent an early stage of microbial invasion of the amniotic cavity with a weak intra-amniotic inflammatory response.
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Affiliation(s)
- Marian Kacerovsky
- Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Sokolska 581, 500 05, Hradec Kralove, Czech Republic.
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.
| | - Jaroslav Stranik
- Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Jana Matulova
- Department of Non-Medical Studies, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Martina Chalupska
- Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Jan Mls
- Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Tomáš Faist
- Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
| | - Helena Hornychova
- Faculty of Medicine in Hradec Kralove, Fingerland's Institute of Pathology, University Hospital Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Rudolf Kukla
- Faculty of Medicine in Hradec Kralove, Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Radka Bolehovska
- Faculty of Medicine in Hradec Kralove, Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Pavel Bostik
- Faculty of Medicine in Hradec Kralove, Institute of Clinical Microbiology, University Hospital Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalization, Institute of Public Health, Oslo, Norway
| | - Ivana Musilova
- Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Sokolska 581, 500 05, Hradec Kralove, Czech Republic
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Maslennikov R, Ivashkin V, Efremova I, Poluektova E, Kudryavtseva A, Krasnov G. Gut dysbiosis and small intestinal bacterial overgrowth as independent forms of gut microbiota disorders in cirrhosis. World J Gastroenterol 2022; 28:1067-1077. [PMID: 35431497 PMCID: PMC8968519 DOI: 10.3748/wjg.v28.i10.1067] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/29/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut dysbiosis and small intestinal bacterial overgrowth (SIBO) are commonly observed in patients with cirrhosis. Despite the substantial number of articles describing the relations between disorders of gut microbiota and various manifestations of cirrhosis, dysbiosis and SIBO were always studied separately.
AIM To study the relationship of gut dysbiosis and SIBO in cirrhosis.
METHODS This observational study included 47 in-patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. SIBO was assessed using the lactulose hydrogen breath test.
RESULTS SIBO was found in 24/47 (51.1%) patients. Patients with SIBO had a higher abundance of Firmicutes (P = 0.017) and Fusobacteria (P = 0.011), and a lower abundance of Bacteroidetes (P = 0.013) than patients without SIBO. This increase in the abundance of Firmicutes occurred mainly due to an increase in the abundance of bacteria from the genus Blautia (P = 0.020) of the Lachnospiraceae family (P = 0.047), while the abundance of other major families of this phylum [Ruminococcaceae (P = 0.856), Peptostreptococcaceae (P = 0.066), Clostridiaceae (P = 0.463), Eubacteriaceae (P = 0.463), Lactobacillaceae (P = 0.413), and Veillonellaceae (P = 0.632)] did not differ significantly between the patients with and without SIBO. Reduced level of Bacteroidetes in samples from patients with SIBO was a result of the decrease in bacterial numbers from all the major families of this phylum [Bacteroidaceae (P = 0.014), Porphyromonadaceae (P = 0.002), and Rikenellaceae (P = 0.047)], with the exception of Prevotellaceae (P = 0.941). There were no significant differences in the abundance of taxa that were the main biomarkers of cirrhosis-associated gut dysbiosis [Proteobacteria (P = 0.790), Bacilli (P = 0.573), Enterobacteriaceae (P = 0.632), Streptococcaceae (P = 0.170), Staphylococcaceae (P = 0.450), and Enterococcaceae (P = 0.873)] between patients with and without SIBO.
CONCLUSION Despite the differences observed in the gut microbiome between patients with and without SIBO, gut dysbiosis and SIBO are most likely independent disorders of gut microbiota in cirrhosis.
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Affiliation(s)
- Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Department of Internal Medicine 1, Сonsultative and Diagnostic Center 2 of the Moscow City Health Department, Moscow 107564, Russia
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Irina Efremova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Anna Kudryavtseva
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Plauzolles A, Toumi E, Bonnet M, Pénaranda G, Bidaut G, Chiche L, Allardet-Servent J, Retornaz F, Goutorbe B, Halfon P. Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies. Front Cell Infect Microbiol 2022; 12:722886. [PMID: 35211421 PMCID: PMC8860989 DOI: 10.3389/fcimb.2022.722886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.
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Affiliation(s)
- Anne Plauzolles
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- *Correspondence: Anne Plauzolles,
| | - Eya Toumi
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- MEPHI, IHU Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Marion Bonnet
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
| | - Guillaume Pénaranda
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
| | - Ghislain Bidaut
- CRCM, Aix‐Marseille Univ U105, Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Marseille, France
| | - Laurent Chiche
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
| | | | - Frédérique Retornaz
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
| | - Benoit Goutorbe
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- CRCM, Aix‐Marseille Univ U105, Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Marseille, France
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Philippe Halfon
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
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Zouiouich S, Mariadassou M, Rué O, Vogtmann E, Huybrechts I, Severi G, Boutron-Ruault MC, Senore C, Naccarati A, Mengozzi G, Kozlakidis Z, Jenab M, Sinha R, Gunter MJ, Leclerc M. Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs. Cancer Epidemiol Biomarkers Prev 2022; 31:305-314. [PMID: 34782392 PMCID: PMC10416615 DOI: 10.1158/1055-9965.epi-21-0188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Colorectal cancer screening programs with fecal sample collection may provide a platform for population-based gut microbiome disease research. We investigated sample collection and storage method impact on the accuracy and stability of the V3-V4 region of the 16S rRNA genes and bacterial quantity across seven different collection methods [i.e., no solution, two specimen collection cards, and four types of fecal immunochemical test (FIT) used in four countries] among 19 healthy volunteers. METHODS Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the most abundant genera, alpha diversity metrics, and the first principal coordinates of the beta diversity matrices to estimate the stability of microbial profiles after storage for 7 days at room temperature, 4°C or 30°C, and after screening for the presence of occult blood in the stool. In addition, accuracy was estimated for samples frozen immediately compared to samples with no solution (i.e., the putative gold standard). RESULTS When compared with the putative gold standard, we observed significant variation for all collection methods. However, interindividual variability was much higher than the variability introduced by the collection method. Stability ICCs were high (≥0.75) for FIT tubes that underwent colorectal cancer screening procedures. The relative abundance of Actinobacteria (0.65) was an exception and was lower for different FIT tubes stored at 30°C (range, 0.41-0.90) and room temperature (range, 0.06-0.94). CONCLUSIONS Paper-based collection cards and different types of FIT are acceptable tools for microbiome measurements. IMPACT Our findings inform on the utility of commonly used fecal sample collection methods for developing microbiome-focused cohorts nested within screening programs.
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Affiliation(s)
- Semi Zouiouich
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France.
| | - Mahendra Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Inge Huybrechts
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France
| | - Gianluca Severi
- Université Paris-Saclay, Université Paris-Sud, Université de Versailles Saint-Quentin-en-Yvelines, Centre de Recherche en Epidémiologie et Santé des Populations, National Institute for Health and Medical Research (INSERM), Villejuif, France
- Department of Statistics, Computer Science and Applications "G. Parenti," University of Florence, Florence, Italy
| | - Marie-Christine Boutron-Ruault
- Université Paris-Saclay, Université Paris-Sud, Université de Versailles Saint-Quentin-en-Yvelines, Centre de Recherche en Epidémiologie et Santé des Populations, National Institute for Health and Medical Research (INSERM), Villejuif, France
| | - Carlo Senore
- Epidemiology and Screening Unit-CPO, University Hospital Città della Salute e della Scienza, Torino, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Turin, Italy
| | - Giulio Mengozzi
- Clinical biochemistry Unit, University Hospital Città della Salute e della Scienza, Turin, Italy
| | - Zisis Kozlakidis
- Laboratory Services and Biobank, International Agency for Research on Cancer-WHO, Lyon, France
| | - Mazda Jenab
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France
| | - Marion Leclerc
- Université Paris Saclay, INRAe, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Goldman SL, Sanders JG, Yan W, Denice A, Cornwall M, Ivey KN, Taylor EN, Gunderson AR, Sheehan MJ, Mjungu D, Lonsdorf EV, Pusey AE, Hahn BH, Moeller AH. Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. Mol Ecol Resour 2022; 22:122-136. [PMID: 34174174 PMCID: PMC8688194 DOI: 10.1111/1755-0998.13456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 01/03/2023]
Abstract
Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.
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Affiliation(s)
- Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14850, USA
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Anthony Denice
- Project Chimps, Morganton, GA 30560, USA
- Present address: Chimpanzee Sanctuary Northwest, Cle Elum, WA 98922, USA
| | - Margaret Cornwall
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Kathleen N. Ivey
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
- Present address: Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Emily N. Taylor
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Alex R. Gunderson
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
| | | | - Elizabeth V. Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, LSP 261B, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, 101 Biological Sciences Building, Duke University, Durham, NC 27708, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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Mordant A, Kleiner M. Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes. Microbiol Spectr 2021; 9:e0187721. [PMID: 34908431 PMCID: PMC8672883 DOI: 10.1128/spectrum.01877-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/31/2021] [Indexed: 12/20/2022] Open
Abstract
A critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for approaches that measure gene expression, such as metaproteomics, which is used to identify and quantify proteins in microbiomes. Intestinal microbiome samples are typically stored by flash-freezing and storage at -80°C, but some experimental setups do not allow for immediate freezing of samples. In this study, we evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible. We collected fecal samples from C57BL/6 mice and stored them for 1 and 4 weeks using the following methods: flash-freezing in liquid nitrogen, immersion in RNAlater, immersion in 95% ethanol, immersion in a RNAlater-like buffer, and combinations of these methods. After storage, we extracted protein and prepared peptides for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis to identify and quantify peptides and proteins. All samples produced highly similar metaproteomes, except for ethanol-preserved samples that were distinct from all other samples in terms of protein identifications and protein abundance profiles. Flash-freezing and RNAlater (or RNAlater-like treatments) produced metaproteomes that differed only slightly, with less than 0.7% of identified proteins differing in abundance. In contrast, ethanol preservation resulted in an average of 9.5% of the identified proteins differing in abundance between ethanol and the other treatments. Our results suggest that preservation at room temperature in RNAlater or an RNAlater-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses. IMPORTANCE Metaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members. A critical step for metaproteomics workflows is preserving samples before analysis because protein profiles are susceptible to fast changes in response to changes in environmental conditions (air exposure, temperature changes, etc.). This study evaluated the effects of different preservation treatments on the metaproteomes of intestinal microbiome samples. In contrast to prior work on preservation of fecal samples for metaproteomics analyses, we ensured that all steps of sample preservation were identical so that all differences could be attributed to the preservation method.
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Affiliation(s)
- Angie Mordant
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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The Use of Flocked Swabs with a Protective Medium Increases the Recovery of Live Brucella spp. and DNA Detection. Microbiol Spectr 2021; 9:e0072821. [PMID: 34787496 PMCID: PMC8597647 DOI: 10.1128/spectrum.00728-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brucellosis is a worldwide zoonosis caused by bacteria from the genus Brucella. Once established, it is very hard to eradicate this disease, since it contaminates animals, the environment, and humans, causing problems for veterinary and public health as well as wildlife protection programs. Swabs are used for sampling in bacteriological and/or molecular diagnostics, from seropositive animals with disease symptoms, from genitalia or tissue lesions, as well as from contaminated environments. The aim of this study was to compare main of the commercially used swab types for sampling and diagnostics of Brucella spp. and determine the optimal storage conditions and time frame for testing. To achieve this, we tested bacterial and molecular methods for detection of Brucella abortus, Brucella melitensis, and Brucella suis using nine swab types, all with different tip materials, treated immediately after spiking, after 72 h at +4°C, and after 72 h at −20°C. Flocked swabs showed the highest capacity to preserve bacterial viability and DNA quality, regardless the storage conditions. Flocked swabs immersed in a protective medium provided the best conditions for Brucella survival in all three storage conditions. At the same time, the efficacy of quantitative PCR (qPCR) detection for all swabs, including the positive control, was above 50%, irrespective of the storage conditions, while bacterial survival was significantly lowered when swabs were kept at +4°C or −20°C for 72 h (48.2% and 27.5%, respectively). Compared to the positive control and other types, the flocked swabs maintained higher reproducibility regarding their capacity to preserve live bacteria in all three storage conditions. IMPORTANCE In order to protect public and veterinary health from highly zoonotic bacteria such as members of the genus Brucella and prevent their dissemination into the environment, direct diagnostics are of utmost importance. However, in addition to the highly specific diagnostic tests, the sampling methods, time necessary for specimens to reach the laboratories, and transport conditions are important factors to consider in order to increase the sensitivity of performed tests, especially bacterial culturing and qPCR. This paper shows how different swab types and storage conditions influence classical bacteriological diagnostics of the most prevalent Brucella species – B. melitensis, B. abortus, and B. suis – but have little impact on molecular methods. The presented results highlight (i) the choice of swab regarding the storage and transport conditions, (ii) the importance of immediate swab treatment upon sampling, and (iii) that molecular methods do not depend on storage conditions, unlike classical bacteriological isolation.
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Kacerovsky M, Matulova J, Andrys C, Mls J, Hornychova H, Kukla R, Bostik P, Burckova H, Spacek R, Jacobsson B, Musilova I. Preterm prelabor rupture of membranes without microbial invasion of the amniotic cavity and intra-amniotic inflammation: a heterogeneous group with differences in adverse outcomes. J Matern Fetal Neonatal Med 2021; 35:9145-9156. [DOI: 10.1080/14767058.2021.2017875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marian Kacerovsky
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jana Matulova
- Department of Non-Medical Studies, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ctirad Andrys
- Institute of Clinical Immunology and Allergy, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Mls
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Helena Hornychova
- Institute of Clinical Microbiology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Rudolf Kukla
- Fingerland’s Institute of Pathology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Pavel Bostik
- Fingerland’s Institute of Pathology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Hana Burckova
- Department of Neonatology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Richard Spacek
- Department of Obstetrics and Gynecology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalization, Institute of Public Health, Oslo, Norway
| | - Ivana Musilova
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
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Jurek L, Sevil M, Jay A, Schröder C, Baghdadli A, Héry-Arnaud G, Geoffray MM. Is there a dysbiosis in individuals with a neurodevelopmental disorder compared to controls over the course of development? A systematic review. Eur Child Adolesc Psychiatry 2021; 30:1671-1694. [PMID: 32385698 DOI: 10.1007/s00787-020-01544-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/24/2020] [Indexed: 12/16/2022]
Abstract
Many scientific papers reported that an unbalanced gut microbiota could lead to or worsen neurodevelopmental disorders (NDD). A dysbiosis may then be observed in the course of development and mark a dysfunction within what is called the gut-brain axis. The aim of this systematic review is to investigate potential evidence of dysbiosis in children and young adults with NDD compared to controls. Using the PRISMA guidelines we systematically reviewed studies that compared the gut microbiota in NDD participants (with an age inferior to thirty) to the gut microbiota of controls, regardless of the data analysis methods used. The MEDLINE, Scopus and PsycINFO databases were searched up to September 2018. 31 studies with a total sample size of 3002 ASD (Autism Spectrum Disorder) and 84 ADHD (Attention Deficit Hyperactivity Disorder) participants were included in this systematic review. Independent data extraction and quality assessment were conducted. The quality of the studies was rated from low to high. Population characterization and experimental methods were highly heterogeneous in terms of the data available, selection of criteria, and dysbiosis measurement. A dysbiosis was reported in 28 studies in terms of either diversity, bacterial composition or metabolome dysfunction. Due to heterogeneity, a quantitative synthesis was not applicable. In this paper, we discuss the different biases to understand the complexity of microbiota and neurodevelopmental disorders to provide leads for future cohort studies looking to answer the questions raised by the trillions of microorganisms that inhabit key body niches.
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Affiliation(s)
- Lucie Jurek
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France.
- Health Services and Performance Research EA7425, Claude Bernard Lyon 1 University (CBL1), Lyon, France.
| | - Marine Sevil
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France
| | - Agathe Jay
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France
| | - Carmen Schröder
- Department of Child and Adolescent Psychiatry, Strasbourg University Hospital, Strasbourg, France
- CNRS UPR 3212, Team 9 Institute of Cellular and Integrative Neurosciences (INCI), Strasbourg, France
| | - Amaria Baghdadli
- Child and Adolescent Psychiatry Departement, Montpellier University Hospital, Montpellier, France
- INSERM U1178 Centre de Recherche en Epidémiologie Et Santé Des Populations (CESP), Paris Sud University (UPS) Et Versailles Saint Quentin University (UVSQ), Versailles, France
| | - Geneviève Héry-Arnaud
- UMR1078, Génétique, Génomique Fonctionnelle Et Biotechnologies, INSERM, Université de Brest, EFS, IBSAM, Brest, France
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, Brest, France
| | - Marie-Maude Geoffray
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France
- Health Services and Performance Research EA7425, Claude Bernard Lyon 1 University (CBL1), Lyon, France
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