Human Microbiome Journal最新文献

{"title":"From anaerobes to aerointolerant prokaryotes","authors":"Sokhna Ndongo ,&nbsp;Saber Khelaifia ,&nbsp;Jean-Christophe Lagier ,&nbsp;Didier Raoult","doi":"10.1016/j.humic.2019.100068","DOIUrl":"10.1016/j.humic.2019.100068","url":null,"abstract":"<div><p>An increasing number of scientists are turning to the microbiota to understand and/or explain the origin of various human metabolic or inflammatory diseases. Oxygen-intolerant bacteria represent the major population of the human intestinal microbiota. Their isolation is often difficult or even fastidious. The number of studies showing their beneficial role in human health is growing exponentially. <em>Faecalibacterium prausnitzii</em> and <em>Akkermansia muciniphila</em> are abundantly represented in healthy intestinal microbiota and their imbalance is positively correlated with inflammatory diseases and metabolic disorders (obesity, diabetes, cancers). Their use as probiotics presents very promising results in restoring the balance of microbial flora but also in the treatment of certain pathological conditions. The Christensenellaceae family has recently emerged as a hereditary taxon and studies have shown that its abundance is positively correlated with leanness and controls obesity in recipient mice. Here, we report the different culture strategies and techniques used for their isolation; the role of antioxidants in the survival of these oxygen-sensitive species in clinical sample and their maintenance in culture isolates.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48768561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut dysbiosis in severe acute malnutrition is not an immaturity: The irreversible quantitative-qualitative paradigm shift","authors":"Matthieu Million ,&nbsp;Didier Raoult","doi":"10.1016/j.humic.2019.100067","DOIUrl":"10.1016/j.humic.2019.100067","url":null,"abstract":"<div><p>We read with interest a work of the Gordon team reporting a gut microbiota immaturity in severe acute malnutrition. However, almost all gut microbes are found in colostrum and breast milk, including methanogenic <em>Archaea.</em> These <em>Archaea</em> are detected in baby’s stomach and in 40% healthy control children but are lost in severe acute malnutrition. <em>Bifidobacterium breve</em> and <em>Bifidobacterium longum</em> are other exceptions to immaturity. These errors are critical because they are a key to treat and cure these children. We argue that milk probiotics including <em>Bifidobacterium, Lactobacillus</em> and <em>Archaea</em> could be the next revolution in the management of malnutrition.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42667734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Is a Fecal Microbiota Transplant Useful for Treating Inflammatory Bowel Disease?","authors":"A. Suceveanu, A. Dumitru, M. Musat, C. Voinea, F. Voinea, I. Parepa, A. Stoian, L. Mazilu, A. Suceveanu","doi":"10.5772/intechopen.91444","DOIUrl":"https://doi.org/10.5772/intechopen.91444","url":null,"abstract":"Ulcerative colitis and Crohn’s disease represent the major groups of idiopathic disorders in inflammatory bowel disease (IBD). The etiology includes environmental factors, genetic factors, and immune responses. The pathogenesis is diversified; however, no guaranteed curative therapeutic regimen has been developed so far. This review contains information related to pathophysiology and current treatment options for IBD. It is known that IBD is caused by tissue-disruptive inflammatory reactions of the gut wall; that is why downregulation of the immune responses allows the healing of the damaged mucosa and allows the resetting of the physiological functions of the gut back to normal. The main treatment options are still corticosteroids, immunomodulators, antibiotics, probiotics, and a series of new agents. Their effects include modulation of cytokines, neutrophil-derived factors, adhesion molecules, and reactive oxygen/nitrogen metabolites. The monoclonal antitumor necrosis factor as infliximab recombinant anti-inflammatory cytokines or related gene therapy is also used nowadays. Still, the fecal microbiota transplantation (FMT) is considered to revolutionize the therapy in IBD, considering the abnormal inflammatory response due to the complicated relationship between microbiota and the immune system. It is imperative to mention the critical role dysbiosis may have in the pathogenesis of IBDs. This review summarizes the available literature concerning the efficacy of FMT in IBDs.","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77954528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The origins of gut microbiome research in Europe: From Escherich to Nissle","authors":"Eulàlia Farré-Maduell ,&nbsp;Climent Casals-Pascual","doi":"10.1016/j.humic.2019.100065","DOIUrl":"10.1016/j.humic.2019.100065","url":null,"abstract":"<div><p>Microbiome research is rapidly changing the way we understand medicine. However, unbeknownst to many, several critical milestones of microbiome research took place in the late 1800s in Europe. In this article, we review the most important contributions in the area of microbiome research by leading scientists in Europe. Following the initial observations of intestinal microorganisms, German paediatrician Theodor Escherich consolidated the study of the human gut flora. His work was continued by Henry Tissier in Paris, who administered probiotic bacteria in children and adults to improve gastrointestinal conditions. Immunologist Ilya Metchnikov popularised the consumption of fermented milk to delay the effects of aging. During WWI, medical microbiologist Alfred Nissle discovered and patented gelatine capsules of <em>E. coli</em> Nissle 1917 to antagonise the effects of harmful intestinal bacteria. The translational potential of this research faded in Western medicine to re-emerge recently in the new light of current microbiome research, with the arrival of rapid and affordable sequencing tools, the Human Microbiome Project and the remarkable efficacy of faecal microbiota transplant to treat some conditions, like <em>Clostridium difficile</em> infection.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100065","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47093753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response to article “A retrospective outcome study of 42 patients with chronic fatigue syndrome, 30 of whom has irritable bowel syndrome. Half were treated with oral approaches, and half were treated with faecal microbiome transplantation”","authors":"Harriet Kingston-Smith,&nbsp;Annabel Clancy,&nbsp;Thomas Borody","doi":"10.1016/j.humic.2019.100064","DOIUrl":"10.1016/j.humic.2019.100064","url":null,"abstract":"","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49076095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in the bacterial profiles of infant gut by birth process, milk diet, and choice of 16S rRNA gene target region","authors":"Maze Ann Biol-Aquino ,&nbsp;Christine Jane Perdiz ,&nbsp;Melissa Borlagdan ,&nbsp;James David Alcantara ,&nbsp;Aida Mallillin","doi":"10.1016/j.humic.2019.100062","DOIUrl":"10.1016/j.humic.2019.100062","url":null,"abstract":"<div><p>Perinatal factors such as birth process and milk diet have been known to greatly influence the development of gut microbiota, which is often studied using amplicon sequencing of the 16S rRNA gene. However, targeting different hypervariable region/s generates variable bacterial community profiles that are critical in the interpretation of results attributed to such influential factors. In this study, we first determined the influence of birth process and milk diet on the bacterial diversity and profiles in the gut of 60 healthy Filipino infants aged 2–4 months old.</p><p>Results reveal the combined influence of birth process and infant milk diet in the establishment and/or shifts of microbial communities in the gut of infants during this age, which blurs out the distinction of microbial community profiles of the infant gut known to one factor alone. On the technical aspect, we elected 10 stool samples from cesarean-delivered exclusively breast-fed infants to be amplified with both V3-V4 and V4-V5 primers and noted differences in the abundance of <em>Firmicutes</em> and <em>Actinobacteri</em>a. Despite variations in the relative abundance of these taxa, we noted that at least 4 of the 10 CD-BF samples share similar enriched taxa with both primer sets used. Hence, the gut microbiota of infants during the age of 2–4 months old is highly dynamic with individualistic bacterial communities that can be critical for dietary mediations.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44121440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of having Christmas dinner with in-laws on gut microbiota composition","authors":"Nicolien C. de Clercq ,&nbsp;Myrthe N. Frissen ,&nbsp;Evgeni Levin ,&nbsp;Mark Davids ,&nbsp;Jorn Hartman ,&nbsp;Andrei Prodan ,&nbsp;Hilde Herrema ,&nbsp;Albert K. Groen ,&nbsp;Johannes A. Romijn ,&nbsp;Max Nieuwdorp","doi":"10.1016/j.humic.2019.100058","DOIUrl":"10.1016/j.humic.2019.100058","url":null,"abstract":"<div><p>The Christmas season can have a major impact on human health. Especially increased contact with in-laws during the holiday season is an important environmental factor known to affect both physical and mental health (Mirza et al., 2004). However, the mechanism through which in-laws influence host health is not yet understood. Emerging evidence has identified the intestinal microbiota as an important mediator for both physical and mental health. Here, we performed a prospective observational study to examine the impact of contact with in-laws on the gut microbiome during the Christmas season. We conducted 16S ribosomal DNA sequencing of fecal samples collected at two separate time points (December 23rd and December 27th 2016) from a group of 28 healthy volunteers celebrating Christmas. To discriminate between participants who visited their own family versus their in-laws, we built a multivariate statistical model that identified microbial biomarker species. We observed two distinct microbial-biomarker signatures discriminating the participants that visited their in-laws versus their own family over the Christmas season. We identified seven bacterial species whose relative-change profile differed significantly among these two groups. In participants visiting in-laws, there was a significant decrease in all <em>Ruminococcus</em> species, known to be associated with psychological stress and depression. A larger randomized controlled study is needed to reproduce these findings before we can recognize in-laws as a potential risk factor for the gut microbiota composition and subsequently host health.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46922114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients","authors":"Tarik Alhmoud ,&nbsp;Anand Kumar ,&nbsp;Chien-Chi Lo ,&nbsp;Rana Al-Sadi ,&nbsp;Stacey Clegg ,&nbsp;Ihab Alomari ,&nbsp;Tarek Zmeili ,&nbsp;Cheryl Diane Gleasne ,&nbsp;Kim Mcmurry ,&nbsp;Armand Earl Ko Dichosa ,&nbsp;Momchilo Vuyisich ,&nbsp;Patrick Sam Guy Chain ,&nbsp;Shiraz Mishra ,&nbsp;Thomas Ma","doi":"10.1016/j.humic.2019.100059","DOIUrl":"10.1016/j.humic.2019.100059","url":null,"abstract":"<div><h3>Background</h3><p>Acute Coronary Syndrome (ACS) is a leading cause of morbidity and mortality. Perturbed gut-microbiota (dysbiosis) and increased intestinal permeability (leaky-gut) with translocation of bacterial antigens, play critical role in obesity and metabolic syndrome, which are also major ACS risk factors. Additionally, Trimethylamine-N-Oxide (TMAO), a metabolite produced by phylum Proteobacteria in gut is implicated in developing ACS. As Proteobacteria is a major source of translocated antigen lipopolysaccharides (LPS), we hypothesized that ACS patients have leaky-gut condition characterized by dysbiosis with increased Proteobacteria, leading to elevated blood levels of TMAO and LPS.</p></div><div><h3>Methods</h3><p>In a pilot case-control study, we enrolled 19 ACS patients (within 72-h of cardiac events) and 19 healthy-controls. Gut barrier function was determined using lactulose-to-mannitol urinary excretion ratio (L/M ratio). Stool microbiome composition was examined using16S sequencing and predictive functional analysis for LPS biosynthesis pathway by PICRUSt tool. Serum TMAO and LPS levels were measured.</p></div><div><h3>Results</h3><p>ACS patients had increased Gammaproteobacteria compared to controls:1.8 ± 3.0 vs. 0.2 ± 0.4% (P = 0.04). Though Proteobacteria level was increased but not statistically significant: 4.1 ± 3.8 vs. 2.1 ± 1.7% (P = 0.056). L/M-ratio was three times higher in ACS patients; 0.06 ± 0.07 vs 0.023 ± 0.02, (P = 0.014). Surprisingly, there was no difference in the mean serum LPS or TMAO levels. However, PICRUSt analysis indicated increased Proteobacteria population increasingly contributed to LPS biosynthesis in ACS patients only.</p></div><div><h3>Conclusions</h3><p>ACS patients likely to have leaky-gut and perturbed gut microbiota. Further studies are required to precisely define the role of dysbiosis in ACS.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43950663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond the gut: Skin microbiome compositional changes are associated with BMI","authors":"Michael Brandwein ,&nbsp;Idan Katz ,&nbsp;Ariel Katz ,&nbsp;Ron Kohen","doi":"10.1016/j.humic.2019.100063","DOIUrl":"10.1016/j.humic.2019.100063","url":null,"abstract":"<div><p>Microbiome compositional changes are associated with obesity in the gut. Emerging evidence points to a connection between gut and skin microbial communities. We hypothesized that skin microbiome compositional changes are associated with different BMI levels and that overweight or obese individuals would have reduced skin microbial diversity. We statistically analyzed gut, oral and skin microbiome samples to recapture previously observed partitioning between the microbiomes of these sites. We further analyzed 822 skin microbiome samples from the American Gut Project database and correlated BMI levels with community structure and composition using QIIME. Gut, oral and skin samples showed distinct community composition, and gut and skin microbial diversity was affected by BMI. Oral microbial diversity was not affected by BMI. Skin beta-diversity and community composition was correlated with BMI category, and <em>Corynebacterium</em> relative abundance was significantly correlated with BMI. In conclusion, non-cutaneous conditions affect the composition of the skin microbiome and the skin microbiome may therefore be used as a biomarker for disease manifestations beyond those with a cutaneous etiology.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48599035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A retrospective outcome study of 42 patients with Chronic Fatigue Syndrome, 30 of whom had Irritable Bowel Syndrome. Half were treated with oral approaches, and half were treated with Faecal Microbiome Transplantation","authors":"J.N. Kenyon ,&nbsp;Shelly Coe ,&nbsp;Hooshang Izadi","doi":"10.1016/j.humic.2019.100061","DOIUrl":"10.1016/j.humic.2019.100061","url":null,"abstract":"<div><p>The gut microbiome comprises the community of microorganisms in the intestinal tract. Research suggests that an altered microbiome may play a role in a wide range of disorders including myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).</p></div><div><h3>Methods</h3><p>42 participants with ME/CFS with Irritable Bowel Syndrome (IBS) were allocated into one of two groups, 21 were treated with standard oral approaches, which centred around various nutritional remedies, probiotics, prebiotics, dietary advice and lifestyle advice. The second group who had mostly failed using oral approaches, were treated with Faecal Microbiome Transplantation (FMT). Each patient received 10 Implants, each from a different screened donor, and the Implants were processed under anaerobic conditions. The transplant is delivered via a paediatric rectal catheter, which is inserted through the anus to reach the lower part of the sigmoid colon.</p><p>The results were assessed on a percentage basis before and after treatment, 0% being no improvement, 100% being maximum improvement. An exact non-parametric Mann-Whitney (one-tailed) test was used to compare medians from those on FMT compared with those receiving oral approaches only. On clinical experience over many years, the only way to judge improvement in Chronic Fatigue Syndrome as there is no test for Chronic Fatigue Syndrome, is my clinical assessment.</p></div><div><h3>Results</h3><p>The median for the FMT group was found to be significantly higher compared to the oral treatment group (Mann-Whitney U = 111.5, p = .003). Therefore, the FMT group improved to a greater extent (z = −2.761).</p></div><div><h3>Conclusion</h3><p>This study shows that FMT is a safe and a promising treatment for CFS associated with IBS. Adequately powered randomised controlled trials should be carried out to assess the effectiveness of FMT in patients with CFS and IBS.</p></div>","PeriodicalId":37790,"journal":{"name":"Human Microbiome Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.humic.2019.100061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43357370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}