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Miller J, Żebrowska-Różańska P, Czajkowska A, Szponar B, Kumala-Ćwikła A, Chmielarz M, Łaczmański Ł. Faecal microbiota and fatty acids in feline chronic enteropathy. BMC Vet Res 2023; 19:281. [PMID: 38124157 PMCID: PMC10731866 DOI: 10.1186/s12917-023-03824-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Feline chronic enteropathy is a set of disorders defined as the presence of clinical signs of gastrointestinal disease for at least three weeks. The most common final diagnoses are inflammatory bowel disease and alimentary small cell lymphoma. The etiopathogenesis of these diseases is incompletely understood; however, it is hypothesised that they involve a combination of factors, including altered composition and/or functionality of the intestinal microbiome. An important factor in the interplay of the microbiome and host is the production of short- and branched-chain fatty acids. The aim of this study was to evaluate the possible differences in faecal microbiota diversity, composition and fatty acid production between cats suffering from chronic enteropathy and healthy cats. Sixteen cats suffering from chronic enteropathy and fourteen healthy control cats were enrolled in the study. The microbiota compositions of faecal samples were analysed by using next-generation amplicon sequencing of the V3V4 fragment of the 16S rRNA gene. Fatty acids were evaluated by high-performance liquid chromatography. RESULTS Both the alpha and beta diversities were significantly lower in samples obtained from cats with chronic enteropathy. The relative abundance of the phylum Proteobacteria, orders Lactobacillales and Enterobacterales, family Enteriobacteriaceae and genus Escherichia Shigella were higher in diseased cats, whereas the abundance of the phylum Bacteroidota and order Peptococcales were higher in control cats. The faecal concentrations of short-chain fatty acids were higher in cats with chronic enteropathy, with lower propionate proportions and higher butyrate proportions. CONCLUSION The study revealed alterations in microbiota compositions and short-chain fatty acid concentration in cats suffering from chronic enteropathy, which is an important finding both for research on the pathogenesis of the disease and for potential therapeutic interventions in the form of faecal microbiota transplantation and/or probiotic supplementation.
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Affiliation(s)
- Julia Miller
- Department of Immunology, Pathophysiology and Veterinary Preventive Medicine, Wroclaw University of Environmental and Life Sciences, Norwida 31, Wroclaw, 50-375, Poland.
| | - Paulina Żebrowska-Różańska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Aleksandra Czajkowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Bogumiła Szponar
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Aleksandra Kumala-Ćwikła
- Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Wroclaw, Poland
| | | | - Łukasz Łaczmański
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Ardalan ZS, Yao CK, Green K, Probert C, Gill PA, Rosella S, Muir JG, Sparrow MP, Gibson PR. A novel Monash Pouch diet in patients with an ileoanal pouch is tolerable and has favorable metabolic luminal effects. JGH Open 2023; 7:942-952. [PMID: 38162853 PMCID: PMC10757501 DOI: 10.1002/jgh3.13008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 01/03/2024]
Abstract
Aims To evaluate a whole-food diet strategy (the Monash Pouch diet [MPD]) designed based on the interacting roles dietary factors play with pouch health. Specifically, its tolerability and acceptability, whether it achieved its dietary and metabolic goals, and the effects on symptoms and inflammation were examined. Methods In a 6-week open-label trial, patients with ileoanal pouches educated on the MPD were assessed regarding diet tolerability and acceptance, food intake (7-day food diaries), pouch-related symptoms (clinical pouchitis disease activity index), and, in 24-h fecal samples, calprotectin, fermentative biomarkers, and volatile organic compounds (VOC). Results Of 12 patients, 6 male, mean (SD) age 55 (5) and pouch age 13 (2) years, one withdrew with partial small bowel obstruction. Tolerability was excellent in 9 (75%) and acceptance was high (81%). Targeted changes in dietary intake were achieved. Fecal branched- to short-chain fatty acid ratio increased by median 60 [IQR: 11-80]% (P = 0.02). Fecal VOCs for 3 compounds were also increased, 2-methyl-5-propan-2-ylcyclohexa-1,3-diene (Fold-change [FC] 2.08), 1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane (FC 3.86), propan-2-ol (FC 2.10). All six symptomatic patients achieved symptomatic remission (P = 0.03). Fecal calprotectin at baseline was 292 [176-527] μg/g and at week 5 was 205 [148-310] μg/g (P = 0.72). Conclusion Well tolerated and accepted, the MPD achieved targeted changes in intakes and fermentation of carbohydrates relative to that of protein. There were signals of improvement in symptoms. These results indicate the need for a randomized-controlled trial. (Trial registration: ACTRN12621000374864; https://www.anzctr.org.au/ACTRN12621000374864.aspx).
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Affiliation(s)
- Zaid S Ardalan
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
| | - Chu K Yao
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
| | - Kraig Green
- Department of Molecular and Clinical Cancer MedicineUniversity of LiverpoolLiverpoolUK
| | - Chris Probert
- Department of Molecular and Clinical Cancer MedicineUniversity of LiverpoolLiverpoolUK
| | - Paul A Gill
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
| | - Sam Rosella
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
| | - Jane G Muir
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
| | - Miles P Sparrow
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
| | - Peter R Gibson
- Department of Gastroenterology, Central Clinical SchoolMonash University and Alfred HealthMelbourneVictoriaAustralia
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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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Superdock DK, Zhang W, Poole AC. Processing and Storage Methods Affect Oral and Gut Microbiome Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544865. [PMID: 37398124 PMCID: PMC10312680 DOI: 10.1101/2023.06.13.544865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Across microbiome studies, fecal and oral samples are stored and processed in different ways, which could affect the observed microbiome composition. Here, we compared treatment methods, which included both storage conditions and processing methods, applied to samples prior to DNA extraction to determine how each affects microbial community diversity as assessed by 16S rRNA gene sequencing. We collected dental swab, saliva, and fecal samples from 10 individuals, with three technical replicates per treatment method. We assessed four methods of processing fecal samples prior to DNA extraction. We also compared different fractions of frozen 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 retained the highest levels of alpha diversity in samples. The supernatant fraction of thawed saliva samples had the second highest alpha diversity compared to fresh. Then we investigated the differences in microbes between different treatments at the domain and phylum levels as well as identified the amplicon sequence variants (ASVs) that were significantly different between the methods producing the highest alpha diversity and the other treatment methods. Lyophilized fecal samples had a greater prevalence of Archaea as well as a greater ratio of Firmicutes to Bacteroidetes compared to the other treatment methods. Our results provide practical considerations, not only for selection of processing method, but also for comparing results across studies that use these methods. Our findings also indicate differences in treatment method could be a confounding factor influencing the presence, absence, or differential abundance of microbes reported in conflicting studies.
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5
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Valdivia-Garcia MA, Chappell KE, Camuzeaux S, Olmo-García L, van der Sluis VH, Radhakrishnan ST, Stephens H, Bouri S, de Campos Braz LM, Williams HT, Lewis MR, Frost G, Li JV. Improved quantitation of short-chain carboxylic acids in human biofluids using 3-nitrophenylhydrazine derivatization and liquid chromatography with tandem mass spectrometry (LC-MS/MS). J Pharm Biomed Anal 2022; 221:115060. [PMID: 36166933 DOI: 10.1016/j.jpba.2022.115060] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 10/31/2022]
Abstract
Short-chain carboxylic acids (SCCAs) produced by gut microbial fermentation may reflect gastrointestinal health. Their concentrations in serum and urine are indicative of specific metabolic pathway activity; therefore, accurate quantitation of SCCAs in different biofluids is desirable. However, it is often challenging to quantitate SCCAs since matrix effects, induced by the presence of a vast variety of other compounds other than SCCAs in complex biofluids, can suppress or enhance signals. Materials used for sample preparation may introduce further analytical challenges. This study reports for the first time a LC-MS/MS-based method to quantitate ten SCCAs (lactate, acetate, 2-hydroxybutyrate, propionate, isobutyrate, butyrate, 2-methylbutyrate, isovalerate, valerate and hexanoate) and evaluates the matrix effects in five human biofluids: serum, urine, stool, and contents from the duodenum and intestinal stoma bags. The optimized method, using 3-Nitrophenylhydrazone as a derivatization agent and a Charge Surface Hybrid reverse phase column, showed clear separation for all SCCAs at a concentration range of 0.1-100 µM, in a 10.5 min run without carry-over effects. The validation of the method showed a good linearity (R2 > 0.99), repeatability (CV ≤ 15%) assessed by intra- and inter-day monitoring. The lowest limit of detection (LLOD) was 25 nM and lowest limit of quantitation (LLOQ) was 50 nM for nine SCCA except acetate at 0.5 and 1 µM, respectively. Quantitative accuracy in all biofluids for most compounds was < ±15%. In summary, this methodology has the advantages over other techniques for its simple and fast sample preparation and a high level of selectivity, repeatability and robustness for SCCA quantification. It also reduced interferences from the matrix or sample containers, making it ideal for use in high-throughput analyses of biofluid samples from large-scale studies.
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Affiliation(s)
- Maria A Valdivia-Garcia
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Katie E Chappell
- The National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Stephane Camuzeaux
- The National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Lucía Olmo-García
- The National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Verena Horneffer van der Sluis
- The National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Shiva T Radhakrishnan
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London W2 1NY, United Kingdom; Section of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Hannah Stephens
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Sonia Bouri
- Inflammatory Bowel Disease Unit, St Mark's Hospital, London HA1 3UJ, United Kingdom
| | - Lucia M de Campos Braz
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Horace T Williams
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London W2 1NY, United Kingdom; Section of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Matthew R Lewis
- The National Phenome Centre, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Gary Frost
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Jia V Li
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom.
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Singh A, Mahajan R, Kahlon BK, Dhaliwal AS, Midha V, Mehta V, Bansal N, Singh D, Sood A. Early fecal microbiome transfer after donor defecation determines response in patients with moderate to severe ulcerative colitis. Indian J Gastroenterol 2022; 41:389-396. [PMID: 36121613 DOI: 10.1007/s12664-022-01257-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/02/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Fecal microbiome transfer (FMT) targeting gut microbiome dysbiosis is an emerging therapy for ulcerative colitis (UC). There is however no consensus on protocols for performing FMT in UC, especially in relation to time after donor feces defecation. METHODS This is a single-center retrospective analysis of patients with moderate-severe UC (total Mayo Clinic score ≥6 and endoscopic Mayo Clinic subscore of ≥2) treated with FMT between September 2017 and December 2019 at Dayanand Medical College and Hospital, Ludhiana, India. Fresh fecal samples from unrelated healthy voluntary donors were administered through colonoscopy at weeks 0, 2, 6, 10, 14, 18, and 22. Time interval between donor feces defecation and FMT procedure was recorded for each FMT session and the mean time of seven sessions was designated aika. Impact of aika on clinical response and safety of FMT was evaluated. RESULTS During the study period, 123 adult patients (mean age 33.75±11.97 years, 61.8% [n=76] males) with moderate-severe UC (mean total Mayo Clinic and endoscopic Mayo Clinic scores 7.49±1.60 and 2.50±0.50, respectively) were treated with FMT. The mean aika was 2.29±0.75 h. The aika was smaller in patients who responded to FMT as compared to non-responders (2.13±0.75 h vs. 2.71±0.76 h, p=0.0002) as well as in patients achieving clinical remission (2.15±0.76 h vs. 2.42±0.76 h, p=0.05). There was no significant impact of aika on adverse effects except for the incidence of borborygmi after FMT, which was higher in patients with aika ≤2 h. CONCLUSION Early FMT after donor feces defecation favorably impacts the clinical response rates in patients with active UC.
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Affiliation(s)
- Arshdeep Singh
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India
| | - Ramit Mahajan
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India
| | | | | | - Vandana Midha
- Department of Internal Medicine, Dayanand Medical College, Ludhiana, 141 001, India
| | - Varun Mehta
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India
| | - Namita Bansal
- Research and Development Centre, Dayanand Medical College, Ludhiana, 141 001, India
| | - Dharmatma Singh
- Research and Development Centre, Dayanand Medical College, Ludhiana, 141 001, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India.
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Button JE, Autran CA, Reens AL, Cosetta CM, Smriga S, Ericson M, Pierce JV, Cook DN, Lee ML, Sun AK, Alousi AM, Koh AY, Rechtman DJ, Jenq RR, McKenzie GJ. Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics. Cell Host Microbe 2022; 30:712-725.e7. [PMID: 35504279 DOI: 10.1016/j.chom.2022.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 11/30/2022]
Abstract
Predictable and sustainable engraftment of live biotherapeutic products into the human gut microbiome is being explored as a promising way to modulate the human gut microbiome. We utilize a synbiotic approach pairing the infant gut microbe Bifidobacterium longum subspecies infantis (B. infantis) and human milk oligosaccharides (HMO). B. infantis, which is typically absent in adults, engrafts into healthy adult microbiomes in an HMO-dependent manner at a relative abundance of up to 25% of the bacterial population without antibiotic pretreatment or adverse effects. Corresponding changes in metabolites are detected. Germ-free mice transplanted with dysbiotic human microbiomes also successfully engraft with B. infantis in an HMO-dependent manner, and the synbiotic augments butyrate levels both in this in vivo model and in in vitro cocultures of the synbiotic with specific Firmicutes species. Finally, the synbiotic inhibits the growth of enteropathogens in vitro. Our findings point to a potential safe mechanism for ameliorating dysbioses characteristic of numerous human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adam K Sun
- Prolacta Bioscience, Duarte, CA 91010, USA
| | - Amin M Alousi
- Department of Stem Cell Transplantation, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Y Koh
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Robert R Jenq
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Giardia duodenalis in a clinically healthy population of captive zoo chimpanzees: Rapid antigen testing, diagnostic real-time PCR and faecal microbiota profiling. Int J Parasitol Parasites Wildl 2022; 17:308-318. [PMID: 35342712 PMCID: PMC8943339 DOI: 10.1016/j.ijppaw.2022.03.007] [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: 01/28/2022] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 02/08/2023]
Abstract
Giardia duodenalis is one of the most common intestinal parasites of humans, with a worldwide distribution. Giardia duodenalis has been reported in both wild and captive populations of non-human primates, namely chimpanzees. In this study we investigated an entire troop of clinically healthy chimpanzees (n = 21) for the presence of G. duodenalis and its association with faecal microbiota profile. Faecal samples (n = 26) were collected from the chimpanzee exhibit from a zoo in Sydney, Australia. Diagnosis of G. duodenalis was made using a Rapid Antigen Test (RAT) as a point-of-care-test and compared to a reference standard real-time PCR test. Approximately half of the chimpanzee faecal samples tested positive for G. duodenalis by both RAT (13/26, 50%) and real-time PCR (14/26, 53.85%). The RAT sensitivity was 85.7% (95% CI: 63.8%–96%) and specificity was 91.7% (95% CI: 68.3%–99%) when compared to the in-house real-time PCR. Genotyping of the samples revealed the presence of zoonotic assemblage B. Microscopic analysis revealed the presence of Troglodytella spp. (14/26), Balantioides sp. (syn. Balantidium sp.) (8/26) as well as Entamoeba spp. (3/26). Microbiota profile based on 16S rRNA gene sequencing revealed that the community was significantly different between G. duodenalis positive and negative samples if RAT results were taken into an account, but not real-time PCR diagnostics results. Proteobacteria and Chloroflexi were the significant features in the dataset that separated G. duodenalis positive and negative samples using LEfSe analysis. Being able to rapidly test for G. duodenalis in captive populations of primates assists in point-of-care diagnostics and may better identify animals with subclinical disease. Under the investigated conditions of the zoo setting, however, presence of G. duodenalis either detected by RAT or real-time PCR was not associated with clinically apparent disease in captive chimpanzees. Whole troop investigation of healthy captive chimpanzees for Giardia duodenalis. Whole chimpanzee troop faecal microbiota profiled. Diagnosing G. duodenalis with Rapid Antigen Test (RAT) as a point-of-care-test. Comparison of RAT and reference real-time PCR test. Presence of G. duodenalis assemblage B.
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Müller B, Rasmusson AJ, Just D, Jayarathna S, Moazzami A, Novicic ZK, Cunningham JL. Fecal Short-Chain Fatty Acid Ratios as Related to Gastrointestinal and Depressive Symptoms in Young Adults. Psychosom Med 2021; 83:693-699. [PMID: 34267089 PMCID: PMC8428857 DOI: 10.1097/psy.0000000000000965] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 04/14/2021] [Indexed: 01/13/2023]
Abstract
OBJECTIVE Short-chain fatty acids (SCFAs) are produced by the gut microbiota and may reflect health. Gut symptoms are common in individuals with depressive disorders, and recent data indicate relationships between gut microbiota and psychiatric health. We aimed to investigate potential associations between SCFAs and self-reported depressive and gut symptoms in young adults. METHODS Fecal samples from 164 individuals (125 were patients with psychiatric disorders: mean [standard deviation] age = 21.9 [2.6] years, 14% men; 39 nonpsychiatric controls: age = 28.5 [9.5] years, 38% men) were analyzed for the SCFA acetate, butyrate, and propionate by nuclear magnetic resonance spectroscopy. We then compared SCFA ratios with dimensional measures of self-reported depressive and gut symptoms. RESULTS Depressive symptoms showed a positive association with acetate levels (ρ = 0.235, p = .003) and negative associations with both butyrate (ρ = -0.195, p = .014) and propionate levels (ρ = -0.201, p = .009) in relation to total SCFA levels. Furthermore, symptoms of diarrhea showed positive associations with acetate (ρ = 0.217, p = .010) and negative associations with propionate in relation to total SCFA levels (ρ = 0.229, p = 0-007). Cluster analysis revealed a heterogeneous pattern where shifts in SCFA ratios were observed in individuals with elevated levels of depressive symptoms, elevated levels of gut symptoms, or both. CONCLUSIONS Shifts in SCFAs are associated with both depressive symptoms and gut symptoms in young adults and may have of relevance for treatment.
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Pérez-Burillo S, Hinojosa-Nogueira D, Navajas-Porras B, Blasco T, Balzerani F, Lerma-Aguilera A, León D, Pastoriza S, Apaolaza I, Planes FJ, Francino MP, Rufián-Henares JÁ. Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments. Nutrients 2021; 13:nu13072207. [PMID: 34199047 PMCID: PMC8308218 DOI: 10.3390/nu13072207] [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: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow’s milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization.
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Affiliation(s)
- Sergio Pérez-Burillo
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Daniel Hinojosa-Nogueira
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
| | - Beatriz Navajas-Porras
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
| | - Telmo Blasco
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Francesco Balzerani
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Alberto Lerma-Aguilera
- Area de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, Spain; (A.L.-A.); (D.L.); (M.P.F.)
| | - Daniel León
- Area de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, Spain; (A.L.-A.); (D.L.); (M.P.F.)
| | - Silvia Pastoriza
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
| | - Iñigo Apaolaza
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Francisco J. Planes
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Maria Pilar Francino
- Area de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, Spain; (A.L.-A.); (D.L.); (M.P.F.)
- CIBER en Epidemiología y Salud Pública, 28001 Madrid, Spain
| | - José Ángel Rufián-Henares
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain
- Correspondence: ; Tel.: +34-958-24-28-41; Fax: +34-958-24-95-77
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Jiang H, Fang S, Yang H, Chen C. Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort. J Anim Sci 2021; 99:6133345. [PMID: 33570553 DOI: 10.1093/jas/skab045] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/05/2021] [Indexed: 12/11/2022] Open
Abstract
Feed efficiency (FE) is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism, and fermentation of dietary indigestible components. Whether and which gut microbes affect FE in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140 d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 operational taxonomic units showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g., Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4, and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high-FE), while 11 bacterial species including 5 Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had a high abundance of the pathways related to amino acid metabolism and biosynthesis, but a low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short-chain fatty acids were determined by UPLC-QTOF/MS and gas chromatography, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving FE in pig production industry.
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Affiliation(s)
- Hui Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, PR China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China
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