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Weh KM, Howard CL, Zhang Y, Tripp BA, Clarke JL, Howell AB, Rubenstein JH, Abrams JA, Westerhoff M, Kresty LA. Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome. JCI Insight 2024; 9:e168112. [PMID: 38329812 PMCID: PMC11063939 DOI: 10.1172/jci.insight.168112] [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: 12/16/2022] [Accepted: 02/02/2024] [Indexed: 02/10/2024] Open
Abstract
The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammation-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett's esophagus, and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities and metabolites contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. Sprague-Dawley rats, with or without reflux induction, received water or C-PAC ad libitum (700 μg/rat/day) for 25 or 40 weeks. C-PAC exerted prebiotic activity abrogating reflux-induced dysbiosis and mitigating bile acid metabolism and transport, culminating in significant inhibition of EAC through TLR/NF-κB/TP53 signaling cascades. At the species level, C-PAC mitigated reflux-induced pathogenic bacteria (Streptococcus parasanguinis, Escherichia coli, and Proteus mirabilis). C-PAC specifically reversed reflux-induced bacterial, inflammatory, and immune-implicated proteins and genes, including Ccl4, Cd14, Crp, Cxcl1, Il6, Il1b, Lbp, Lcn2, Myd88, Nfkb1, Tlr2, and Tlr4, aligning with changes in human EAC progression, as confirmed through public databases. C-PAC is a safe, promising dietary constituent that may be utilized alone or potentially as an adjuvant to current therapies to prevent EAC progression through ameliorating reflux-induced dysbiosis, inflammation, and cellular damage.
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Affiliation(s)
- Katherine M. Weh
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Connor L. Howard
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Yun Zhang
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Jennifer L. Clarke
- Department of Statistics, Department of Food Science Technology, Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Amy B. Howell
- Marucci Center for Blueberry and Cranberry Research, Rutgers University, Chatsworth, New Jersey, USA
| | - Joel H. Rubenstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- LTC Charles S. Kettles Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Maria Westerhoff
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura A. Kresty
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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2
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González A, Fullaondo A, Odriozola A. Techniques, procedures, and applications in microbiome analysis. ADVANCES IN GENETICS 2024; 111:81-115. [PMID: 38908906 DOI: 10.1016/bs.adgen.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microbiota is a complex community of microorganisms living in a defined environment. Until the 20th century, knowledge of microbiota was partial, as the techniques available for their characterization were primarily based on bacteriological culture. In the last twenty years, the development of DNA sequencing technologies, multi-omics, and bioinformatics has expanded our understanding of microorganisms. We have moved from mainly considering them isolated disease-causing agents to recognizing the microbiota as an essential component of host biology. These techniques have shown that the microbiome plays essential roles in various host phenotypes, influencing development, physiology, reproduction, and evolution. This chapter provides researchers with a summary of the primary concepts, sample collection, experimental techniques, and bioinformatics analysis commonly used in microbiome research. The main features, applications in microbiome studies, and their advantages and limitations are included in each section.
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Affiliation(s)
- Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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3
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Kok CR, Mulakken N, Thissen JB, Grey SF, Avila-Herrera A, Upadhyay MM, Lisboa FA, Mabery S, Elster EA, Schobel SA, Be NA. Targeted metagenomic assessment reflects critical colonization in battlefield injuries. Microbiol Spectr 2023; 11:e0252023. [PMID: 37874143 PMCID: PMC10714869 DOI: 10.1128/spectrum.02520-23] [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: 06/16/2023] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Microbial contamination in combat wounds can lead to opportunistic infections and adverse outcomes. However, current microbiological detection has a limited ability to capture microbial functional genes. This work describes the application of targeted metagenomic sequencing to profile wound bioburden and capture relevant wound-associated signatures for clinical utility. Ultimately, the ability to detect such signatures will help guide clinical decisions regarding wound care and management and aid in the prediction of wound outcomes.
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Affiliation(s)
- Car Reen Kok
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Nisha Mulakken
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Scott F. Grey
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Meenu M. Upadhyay
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Felipe A. Lisboa
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Shalini Mabery
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Eric A. Elster
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Seth A. Schobel
- Surgical Critical Care Initiative (SC2i), Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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4
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Gomes N, Ferreira-Sa L, Alves N, Dallago B, Moraes A, Carvalho JL, Nitz N, Hagström L, Braz S, Machado ER, Gurgel-Gonçalves R, Hecht M. Uncovering the effects of Giardia duodenalis on the balance of DNA viruses and bacteria in children's gut microbiota. Acta Trop 2023; 247:107018. [PMID: 37673134 DOI: 10.1016/j.actatropica.2023.107018] [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: 07/03/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023]
Abstract
The neglected parasitosis giardiasis is one of the most common intestinal infections worldwide, affecting mainly infants and young children. Giardia duodenalis may disturb the local microbiome, leading to intestinal ecosystem disorders, and altering different processes in the host, such as the immune response. Nevertheless, the alterations promoted by G. duodenalis on the human gut microbiome have not been thoroughly investigated. Here, we characterized the gut microbiota of G. duodenalis-infected children and determine the main alterations promoted by the parasite. To do so, fecal samples of 26 infected and four uninfected children aged 2 to 6 years old were processed for High Efficiency Microarray analysis, in order to describe their bacterial and viral profiles. Then, we quantified the total bacterial population by qPCR and assessed fecal calprotectin levels, which are closely related with gut inflammation. A total of 286 bacteria's species and 17 viruses' strains were identified. Our results revealed no statistically significant differences between G. duodenalis positive and negative groups in the taxa's phyla and families. However, bacterial species diversity was increased in children infected with G. duodenalis (p < 0.05), while the total number of bacteria was decreased (p < 0.05). Considering the virome analysis, 17 different strains were identified, 88% being bacteriophages. The correlation analysis revealed an important disruption in the balance of DNA virus and bacteria within the intestinal microbiota of Giardia-positive children. Our findings constitute the first description of the gut virome of Giardia-infected children and suggest that G. duodenalis infection exerts a modulatory effect on the gut microbiome, promoting local inflammation and altering the equilibrium of the parasite-microbiota-host triad. This highlights the importance of considering polymicrobial associations and understanding the broader context of giardiasis. Overall, our study provides new insights into the complex interactions between intestinal parasites and the microbiota, which may have implications for the development of novel therapeutic interventions in the future.
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Affiliation(s)
- Nélio Gomes
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Lana Ferreira-Sa
- Laboratory of Medical Parasitology and Vector Biology Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Nayra Alves
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Bruno Dallago
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Aline Moraes
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Juliana Lott Carvalho
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil; Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil
| | - Nadjar Nitz
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Luciana Hagström
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Shélida Braz
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Eleuza Rodrigues Machado
- Laboratory of Medical Parasitology and Vector Biology Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Rodrigo Gurgel-Gonçalves
- Laboratory of Medical Parasitology and Vector Biology Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Mariana Hecht
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil.
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5
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Weh KM, Howard CL, Zhang Y, Tripp BA, Clarke JL, Howell AB, Rubenstein JH, Abrams JA, Westerhoff M, Kresty LA. Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554315. [PMID: 37662411 PMCID: PMC10473615 DOI: 10.1101/2023.08.22.554315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammatory-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett's esophagus and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities and metabolites contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. Sprague Dawley rats, with or without reflux-induction received water or C-PAC ad libitum (700 µg/rat/day) for 25 or 40 weeks. C-PAC exerted prebiotic activity abrogating reflux-induced dysbiosis, and mitigating bile acid metabolism and transport, culminating in significant inhibition of EAC through TLR/NF-κB/P53 signaling cascades. At the species level, C-PAC mitigated reflux-induced pathogenic bacteria (Clostridium perfringens, Escherichia coli, and Proteus mirabilis). C-PAC specifically reversed reflux-induced bacterial, inflammatory and immune-implicated proteins and genes including Ccl4, Cd14, Crp, Cxcl1, Il6, Il1β, Lbp, Lcn2, Myd88, Nfkb1, Tlr2 and Tlr4 aligning with changes in human EAC progression, as confirmed through public databases. C-PAC is a safe promising dietary constituent that may be utilized alone or potentially as an adjuvant to current therapies to prevent EAC progression through ameliorating reflux-induced dysbiosis, inflammation and cellular damage.
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6
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Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem. Sci Rep 2023; 13:4056. [PMID: 36906688 PMCID: PMC10008532 DOI: 10.1038/s41598-023-30916-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.
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Arena-Ortiz ML, Sánchez-Rodríguez EC, Apodaca-Hernández JE, Ortiz-Alcántara JM, Ríos-Contreras K, Chiappa-Carrara X. DNA microarrays to identify etiological agents, as sensors of environmental wellbeing. Front Bioeng Biotechnol 2023; 11:1085976. [PMID: 37168612 PMCID: PMC10165067 DOI: 10.3389/fbioe.2023.1085976] [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: 10/31/2022] [Accepted: 03/28/2023] [Indexed: 05/13/2023] Open
Abstract
Background: The epidemiologic transition in Mexico has generated a change of paradigm in public health. Morbidity is characterized by infectious diseases and the mortality is due to chronic degenerative diseases. The three most important infectious diseases in the country are: respiratory infections, diarrhea, and urinary tract infections. Method: The objective of this work was to build a tool to monitor the presence of health risks in the environment in a timely manner and to demonstrate its application in different sicknesses, especially those that are water related. In this study, we analyzed water samples from five cenotes with high tourist flow in the State of Yucatan. We developed a DNA microarray for the adequate and prompt detection of viruses, bacteria, fungi, and parasites. This microarray could be used in samples of different origin including air, water (fresh, brackish and saltwater), food, inert surfaces or wounds. Clinically, it would allow prompt and precise detection of etiological agents of infectious diseases to prevent outbreaks. It would also be useful for the identification of those agents that cannot be detected in our laboratories with the traditional methods. It includes 38,000 probes that detect 252 etiological agents of diseases in humans and antimicrobial resistance genes. Results from DNA samples can be obtained in 24 h, which would be difficult or impossible using other technologies. Results: The results are readily available within 24 h. Samples from five cenotes (sinkholes) with high flow of people, were analyzed with the microarray. The water samples analyzed detected 228 different bacteria, viruses, fungi, and protozoa. They are amongst the most important etiological agents for infectious diseases in Mexico. Conclusions: The microarray provides the opportunity for precise and early detection of various infectious agents in individuals, hospitals and natural environments. This could help reduce the global burden of diseases, the severity of outbreaks, and reduce antibiotic resistance.
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Affiliation(s)
- María Leticia Arena-Ortiz
- Ecogenomics Laboratory, National Autonomous University of Mexico (UNAM), Yucatan, Mexico
- *Correspondence: María Leticia Arena-Ortiz,
| | - Ernesto Cuauhtemoc Sánchez-Rodríguez
- Hyperbaric Medicine Department at Hospital Agustín O’Horan, Health Ministry of Yucatán, Postgraduate Department of Faculty of Medicine of National Autonomous University of Mexico (UNAM), and Global Health Institute, Michigan State University (MSU), Mérida, Mexico
| | | | | | - Karen Ríos-Contreras
- Ecogenomics Laboratory, National Autonomous University of Mexico (UNAM), Yucatan, Mexico
| | - Xavier Chiappa-Carrara
- Conservation Biology Laboratory, National Autonomous University of Mexico (UNAM), Yucatan, Mexico
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8
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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections. PLoS One 2022; 17:e0278543. [PMID: 36455065 PMCID: PMC9714956 DOI: 10.1371/journal.pone.0278543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae, were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results.
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Pre-transplant Ratio of Firmicutes/Bacteroidetes of Gut Microbiota as a Potential Biomarker of Allograft Rejection in Renal Transplant Recipients. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The advent of technologies has made allogenic transplantation a potential curative therapy for end-stage renal diseases, but the episodes of rejection still remain as one of the challenges in the post-transplant scenario. In the recent years, several human and animal studies have elucidated that gut microbial dysbiosis is closely linked with allogenic transplantation and post-transplant complications. But most of the studies focused on the use of high through-put sequencing technologies to analyze gut microbiota despite of its high cost, analysis and time constraints. Hence, in this work we aimed to study the impact of the two dominant gut phyla Firmicutes and Bacteroidetes on 38 renal transplant recipients, before and after transplantation and to find its association with allograft rejection. Significant changes (p<0.01) were observed in the relative abundances of the phyla Firmicutes and Bacteroidetes at pre- and post-transplant period. We have also found that the recipients who had an increase in Firmicutes/Bacteroidetes (F/B) ratio before transplant were highly prone to rejection in the first-year post-transplant. The Receiver Operating Characteristic (ROC) curve analysis has shown that the ratio of F/B were able to discriminate between rejection and non-rejection cases with an Area under the ROC Curve (AUC) of 0.91. Additionally, we observed that the ratio of F/B have reduced during the time of rejection postulating that gut microbial dysbiosis has more association with rejection. Thus, the assessment of F/B ratio using qPCR would be of a more practical approach for diagnosis and monitoring of graft function in a cost-effective and timely manner.
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10
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Djemiel C, Dequiedt S, Karimi B, Cottin A, Horrigue W, Bailly A, Boutaleb A, Sadet-Bourgeteau S, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L, Terrat S. Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production. Front Microbiol 2022; 13:889788. [PMID: 35847063 PMCID: PMC9280627 DOI: 10.3389/fmicb.2022.889788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/06/2022] [Indexed: 01/02/2023] Open
Abstract
Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity-the backbone of the regulation of ecosystem services and "soil health" maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Battle Karimi
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Novasol Experts, Dijon, France
| | - Aurélien Cottin
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Ali Boutaleb
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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11
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Morrison MD, Thissen JB, Karouia F, Mehta S, Urbaniak C, Venkateswaran K, Smith DJ, Jaing C. Investigation of Spaceflight Induced Changes to Astronaut Microbiomes. Front Microbiol 2021; 12:659179. [PMID: 34149649 PMCID: PMC8207296 DOI: 10.3389/fmicb.2021.659179] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/05/2021] [Indexed: 12/26/2022] Open
Abstract
The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts’ time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts’ saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts’ time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut’s microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.
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Affiliation(s)
- Michael D Morrison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - James B Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Fathi Karouia
- KBRwyle, NASA Ames Research Center, Moffett Field, CA, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States.,Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States
| | - Satish Mehta
- JesTech, NASA Johnson Space Center, Houston, TX, United States
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, NASA-Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, NASA-Jet Propulsion Laboratory, Pasadena, CA, United States
| | - David J Smith
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, United States
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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12
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Modernization of Control of Pathogenic Micro-Organisms in the Food-Chain Requires a Durable Role for Immunoaffinity-Based Detection Methodology-A Review. Foods 2021; 10:foods10040832. [PMID: 33920486 PMCID: PMC8069916 DOI: 10.3390/foods10040832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 01/03/2023] Open
Abstract
Food microbiology is deluged by a vastly growing plethora of analytical methods. This review endeavors to color the context into which methodology has to fit and underlines the importance of sampling and sample treatment. The context is that the highest risk of food contamination is through the animal and human fecal route with a majority of foodborne infections originating from sources in mass and domestic kitchens at the end of the food-chain. Containment requires easy-to-use, failsafe, single-use tests giving an overall risk score in situ. Conversely, progressive food-safety systems are relying increasingly on early assessment of batches and groups involving risk-based sampling, monitoring environment and herd/flock health status, and (historic) food-chain information. Accordingly, responsible field laboratories prefer specificity, multi-analyte, and high-throughput procedures. Under certain etiological and epidemiological circumstances, indirect antigen immunoaffinity assays outperform the diagnostic sensitivity and diagnostic specificity of e.g., nucleic acid sequence-based assays. The current bulk of testing involves therefore ante- and post-mortem probing of humoral response to several pathogens. In this review, the inclusion of immunoglobulins against additional invasive micro-organisms indicating the level of hygiene and ergo public health risks in tests is advocated. Immunomagnetic separation, immunochromatography, immunosensor, microsphere array, lab-on-a-chip/disc platforms increasingly in combination with nanotechnologies, are discussed. The heuristic development of portable and ambulant microfluidic devices is intriguing and promising. Tant pis, many new platforms seem unattainable as the industry standard. Comparability of results with those of reference methods hinders the implementation of new technologies. Whatever the scientific and technological excellence and incentives, the decision-maker determines this implementation after weighing mainly costs and business risks.
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13
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Han X, Liu Y, Yin J, Yue M, Mu Y. Microfluidic devices for multiplexed detection of foodborne pathogens. Food Res Int 2021; 143:110246. [PMID: 33992358 DOI: 10.1016/j.foodres.2021.110246] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 01/10/2023]
Abstract
The global burden of foodborne diseases is substantial and foodborne pathogens are the major cause for human illnesses. In order to prevent the spread of foodborne pathogens, detection methods are constantly being updated towards rapid, portable, inexpensive, and multiplexed on-site detection. Due to the nature of the small size and low volume, microfluidics has been applied to rapid, time-saving, sensitive, and portable devices to meet the requirements of on-site detection. Simultaneous detection of multiple pathogens is another key parameter to ensure food safety. Multiplexed detection technology, including microfluidic chip design, offers a new opportunity to achieve this goal. In this review, we introduced several sample preparation and corresponding detection methods on microfluidic devices for multiplexed detection of foodborne pathogens. In the sample preparation section, methods of cell capture and enrichment, as well as nucleic acid sample preparation, were described in detail, and in the section of detection methods, amplification, immunoassay, surface plasmon resonance and impedance spectroscopy were exhaustively illustrated. The limitations and advantages of all available experimental options were also summarized and discussed in order to form a comprehensive understanding of cutting-edge technologies and provide a comparative assessment for future investigation and in-field application.
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Affiliation(s)
- Xiaoying Han
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China; College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuanhui Liu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China; College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China
| | - Min Yue
- Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, PR China; Hainan Institute of Zhejiang University, Sanya 572025, PR China.
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China.
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14
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An YZ, Ko KA, Kim CS, Gruber R, Wang X, Lee JS. Do periodontal defects affect periodontal inflammation and destruction? Histological/microbiological changes and gene expression profiles of a pilot study in beagle dogs. J Periodontol 2020; 92:1007-1017. [PMID: 33128228 DOI: 10.1002/jper.20-0508] [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: 07/23/2020] [Revised: 09/06/2020] [Accepted: 09/24/2020] [Indexed: 11/12/2022]
Abstract
BACKGROUND The present study focused on the inflammatory disease progress after periodontal defect induction and aimed to specifically determine periodontal tissue responses following dental plaque accumulation by ligatures on a site with/without standardized periodontal defect induction. METHODS After 1 month from extraction of the adjacent teeth, semi-circumferential defects were surgically created in the unilateral second and fourth premolars (test group), whereas no defects were being induced at the contralateral sites (control group). One week later, silk was used to ligate the tooth cervix at both sites to encourage the accumulation of dental plaque. Four weeks later, the tissue samples were collected for histological/histomorphometric and microarray analysis. Microbiological analysis was performed before defect induction and at ligatures, and after 4 weeks of dental plaque accumulation. RESULTS Remarkable inflammation was clinically and histologically observed in both groups after plaque accumulation, and the intrabony type of periodontal defect exaggerated inflammatory cell infiltration into the connective tissue layer. Expression of genes related to inflammation such as IL-1 was highly up-regulated in test sites. However, these inflammatory infiltrations did not invade to a boundary of periodontal ligament and connective tissue attachment in both groups, and histomorphometric results corresponds to these observational results. Bacterial findings also showed no significant differences in detected microbiome compositions between control and test groups at three-time points. CONCLUSION Intrabony defect might exaggerate the plaque-induced inflammation in the aspect of inflammatory cell infiltration and the related gene expression, but both dental plaque and the pre-existing periodontal defect negligibly disrupt periodontal attachment and the underlying alveolar bone.
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Affiliation(s)
- Yin-Zhe An
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Periodontology, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Kyung-A Ko
- Department of Periodontology, College of Dentistry, Research Institute for Periodontal Regeneration, Yonsei University, Seoul, Republic of Korea
| | - Chang-Sung Kim
- Department of Periodontology, College of Dentistry, Research Institute for Periodontal Regeneration, Yonsei University, Seoul, Republic of Korea
| | - Reinhard Gruber
- Department of Oral Biology, School of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Xinhong Wang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Periodontology, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jung-Seok Lee
- Department of Periodontology, College of Dentistry, Research Institute for Periodontal Regeneration, Yonsei University, Seoul, Republic of Korea
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15
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Kurina I, Popenko A, Klimenko N, Koshechkin S, Chuprikova L, Filipenko M, Tyakht A, Alexeev D. Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa. Mol Cell Probes 2020; 52:101570. [PMID: 32304824 PMCID: PMC7158812 DOI: 10.1016/j.mcp.2020.101570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
Abstract
Nowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods - the platform and high-throughput 16S rRNA sequencing - across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.
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Affiliation(s)
- Irina Kurina
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia,Atlas Biomed Group, 31 Malaya Nikitskaya str., 121069, Moscow, Russia,Corresponding author. Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia.
| | - Anna Popenko
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia,Atlas Biomed Group, 31 Malaya Nikitskaya str., 121069, Moscow, Russia
| | - Natalia Klimenko
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova str., 119334, Moscow, Russia
| | - Stanislav Koshechkin
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia
| | - Liubov Chuprikova
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev ave., Novosibirsk, 630090, Russia
| | - Alexander Tyakht
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova str., 119334, Moscow, Russia
| | - Dmitry Alexeev
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia,Atlas Biomed Group, 31 Malaya Nikitskaya str., 121069, Moscow, Russia
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Lekang K, Lanzén A, Jonassen I, Thompson E, Troedsson C. Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments. MARINE POLLUTION BULLETIN 2020; 154:111102. [PMID: 32319925 DOI: 10.1016/j.marpolbul.2020.111102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have applied a prototype version of a phylogenetic microarray to assess the eukaryote community structures of marine sediments from an area with ongoing oil and gas drilling activity. The results were compared with data from both sequencing (metabarcoding) and morphology-based monitoring to evaluate whether microarrays were capable of detecting ecosystem disturbances. A significant correlation between microarray data and chemical pollution indicators, as well as sequencing-based results, was demonstrated, and several potential indicator organisms for pollution-associated parameters were identified, among them a large fraction of microorganisms not covered by traditional morphology-based monitoring. This suggests that microarrays have a potential in future environmental monitoring.
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Affiliation(s)
- Katrine Lekang
- Department of Biology, University of Bergen, Bergen, Norway; Department of Pharmacy, University of Oslo, Norway.
| | - Anders Lanzén
- AZTI-Tecnalia, Marine Research Division, Pasaia, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Eric Thompson
- Department of Biology, University of Bergen, Bergen, Norway; Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway; NORCE, Bergen, Norway
| | - Christofer Troedsson
- Department of Biology, University of Bergen, Bergen, Norway; NORCE, Bergen, Norway; Ocean Bergen AS, Bergen, Norway
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Kao HF, Wang YC, Tseng HY, Wu LSH, Tsai HJ, Hsieh MH, Chen PC, Kuo WS, Liu LF, Liu ZG, Wang JY. Goat Milk Consumption Enhances Innate and Adaptive Immunities and Alleviates Allergen-Induced Airway Inflammation in Offspring Mice. Front Immunol 2020; 11:184. [PMID: 32132998 PMCID: PMC7040033 DOI: 10.3389/fimmu.2020.00184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/23/2020] [Indexed: 11/13/2022] Open
Abstract
Goat milk (GM), as compared to cow milk (CM), is easier for humans to digest. It also has antioxidant and anti-inflammatory effects and can improve minor digestive disorders and prevent allergic diseases in infants. It is unclear whether GM consumed in pregnant mothers has any protective effects on allergic diseases in infants. In this experimental study with mice, we found GM feeding enhanced immunoglobulin production, antigen-specific (ovalbumin, OVA) immune responses, and phagocytosis activity. The GM-fed mice had an increasing proportion of CD3+ T lymphocytes in the spleen. Splenocytes isolated from these animals also showed significantly increased production of cytokines IFN-γ and IL-10. More importantly, GM feeding during pregnancy and lactation periods can confer protective activity onto offspring by alleviating the airway inflammation of allergic asthma induced by mite allergens. There was a remarkably different composition of gut microbiota between offspring of pregnant mice fed with water or with milk (GM or CM). There was a greater proportion of beneficial bacterial species, such as Akkermansia muciniphila, Bacteroides eggerthii, and Parabacteroides goldsteinii in the gut microbiota of offspring from GM- or CM-fed pregnant mice compared to the offspring of water-fed pregnant mice. These results suggested that improving the nutrition of pregnant mice can promote immunological maturation and colonization of gut microbiota in offspring. This mother-to-child biological action may provide a protective effect on atopy development and alleviate allergen-induced airway inflammation in offspring.
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Affiliation(s)
- Hui-Fang Kao
- Department of Nursing, National Tainan Junior College of Nursing, Tainan, Taiwan
| | - Yu-Chin Wang
- Center for Allergy and Clinical Immunology Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsiu-Ying Tseng
- Center for Allergy and Clinical Immunology Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | - Hui-Ju Tsai
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Miao-Hsi Hsieh
- Graduate Institute of Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Chi Chen
- Graduate Institute of Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Shou Kuo
- Center for Allergy and Clinical Immunology Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,School of Chemistry and Materials Science, Nanjing University of Information Science and Technology, Nanjing, China
| | - Li-Fan Liu
- Institute of Gerontology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Zhi-Gang Liu
- Department of Respirology and Allergy, Third Affiliated Hospital of Shengzhen University, Shengzhen, China
| | - Jiu-Yao Wang
- Center for Allergy and Clinical Immunology Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
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