Human Microbiome Journal最新文献

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is estimated to afflict hundreds of thousands, if not millions, of Americans with vastly more impacted individuals worldwide; however, the etiology of this disease has not been well established. Based on the features of ME/CFS, we hypothesized an unrecognized vascular infection may be involved. To evaluate this possibility, we performed a blinded pilot study of 30 ME/CFS patients meeting the Fukuda criteria and 48 normal controls. A community-wide analysis using next-generation DNA sequencing methods detected prokaryotic and eukaryotic populations in the peripheral blood of both ME/CFS patients and normal controls. Analysis of the prokaryotic portion of the samples revealed that organisms belonging to the Pseudomonas asplenii species, Pseudomonadaceae family, Pseudomonadales order, and γ-proteobacteria class are inversely correlated with RAND-36 scores, a quality of life metric that is reduced in ME/CFS patients. In addition, analysis of the detected eukaryotic species suggests that the Perkinsus genus is also inversely associated with RAND-36 scores. The most frequently observed eukaryotic DNA was for Funneliformis mosseae, an arbuscular mycorrhizal fungus, which was in both ME/CFS and normal control samples. A multivariate composite score consisting of the Perkinsus genus, Spumella genus, and β-proteobacteria class displays an inverse relationship to RAND-36 scores. Lastly, the combined measurements of several taxa allow for a retrospective categorical sorting of ME/CFS patients from normal control samples. These results suggest that microbial DNA signatures, including those from poorly understood eukaryotes, may be differentially detectable in ME/CFS and normal control samples.

The infant gut microbiome is rapidly colonized by bacteria from the environment after birth, and this gut ecosystem can facilitate expansion of potential pathogens. Human milk shapes the infant gut microbiome and has evolved to foster the growth of specific bacteria. Breastfed infants fed the coevolved infant gut symbiont Bifidobacterium longum subsp. infantis EVC001 had significant modifications to their gut metagenome, including a decreased number of virulence factor genes.

The gut microbiota is an ecosystem including all bacterial species that permanently colonize the gastro intestinal tract and a large number of other microorganisms from the environment. These millions of microorganisms may be unbalanced by a number of external and internal factors. The aim of this review is to summarize recent findings on animal and human studies on the effect of dietary and geographical provenance on gut microbiota-composition. It includes results on the influence of dietary products, type of diet (e.g. vegetarian and omnivorous subgroups), and geographic areas, as well as differences between populations within the same area. In animal models, most results showed contradictory effects on modulation of the intestinal microbiota within the same phylum, while in human studies, dietary products, such as fat, are often reported as being associated with an increase in Bacteroidetes and Actinobacteria species and a decrease in those in the Firmicutes and Proteobacteria phylum. The results of different studies showed that the omnivorous group has a higher diversity of bacteria compared to vegetarians. Gut microbiota composition differs widely between different areas and between different ethnic groups within the same area. However, a higher diversity of bacteria species was encountered in the African population. The conclusions highlight that gut microbiota composition differs according to diet and eating habits which are closely correlated to geographical location suggesting therefore, the need for more in-depth research, looking at ethnic diversity and eating habits.

Beyond host genetics, the environment determines microbiota-immunity interactions. Most recent studies have focused on the interconnections between micronutrients, microbial and immune populations. However, the control of the gut oxidative stress and redox status has been neglected. Oxidative stress sensitive (Ox-S) prokaryotes include butyrate producers and minority mucosa-associated immunogenic symbionts, such as specific Lactobacillus strains, Bifidobacterium adolescentis, and segmented filamentous bacteria which exemplify the mucosal “minority report” paradigm. Butyrate, produced by Lachnospiraceae, Ruminococcaceae and Bacteroidetes, is the main microbiota-derived gut mucosal immunity regulator and the best functional marker of the healthy mature anaerobic gut microbiota (HMAGM). Oxidative stress during the “window of opportunity” around weaning is observed in severe acute malnutrition and results in Ox-S prokaryote depletion, HMAGM disruption, collapse of butyrate production and durable gut mucosal immunity alteration. High saturated-fat diet leads to oxidative stress, selection of oxidative stress-resistant (Ox-R) Lactobacillus reuteri strains in Peyer’s patches, secretion of pro-inflammatory cytokines, disruption of mucosal immune compartmentalization (leaky gut) and obesity. Beyond dietary micronutrient diversity and pathogen control, future research should focus on antioxidants, control of oxidative stress and Ox-S gut prokaryote preservation as new instrumental targets for maintenance of the gut microbiota-immunity symbiotic loop and prevention of malnutrition and obesity.

Clostridium botulinum is a foodborne bacterium capable of producing a potent botulinum neurotoxin with seven serotypes (A–G). Type A strains are being a great concern for causing foodborne, infant and wound botulism in worldwide. Antibacterial resistance is a not a big problem for treating diseases caused by this organism, but antitoxin treatment available today has not been reverse the paralysis. C. botulinum strain Hall A Sanger is a clinically important strain studied intensively for its biochemical and molecular characteristics. Gene cluster for botulinum toxin is strain-specific in nature, which might have evolved independently of each other. Type A strains have a common mechanism for transcription and metabolic regulation of botulinum toxin. BotR is a known transcriptional regulator that controls the expression of botulinum toxin in type A strains in response to nutritional factors in the gut. Two-component system is a key regulator required for the full virulence of this bacterium underlying response to the host and environmental factors. Amino-acid induced germination and chitin catabolic systems are firmly established in this organism, performing the separate processes of toxin or virulence factor synthesis, sporulation and germination. Several virulence factors have recently been identified from this genome, but molecular function of them in the gut of humans is not yet to be known. Genome-scale models are being as an integrated knowledge base for detailed understanding of its host-microbe interactions during the intoxication process.

Childhood and adolescent obesity is a significant public health concern and has been associated with cardiovascular disease and related metabolic sequelae later in life. In recent years, several studies have postulated an imbalance in the composition of the early life gut microbiota results in pediatric obesity and its associated diseases. The early life gut microbiota is influenced by several factors including the mode of delivery, prematurity, breastfeeding, and the use of antibiotics and probiotics. It has been proposed that, when given early in life, antibiotics and probiotics disrupt the gut microbiota and consequently its metabolic activity, promoting weight gain. Probiotics have increasingly been administrated to children and studies on the perinatal use of probiotics on low birth weight and healthy infants revealed significantly increased body length and weight later in life in comparison with infants who did not receive probiotic supplements. Similarly, exposure to antibiotics is very high perinatally and in the early periods of life and there is evidence that antibiotic treatment decreases the biodiversity of the early life gut microbiota. In addition, studies have revealed that antibiotic treatment during the first months of life is associated with being overweight later in life. In this paper we review the effects of the administration of probiotics and antibiotics in early life on the gut microbiota and discuss their effects on weight gain.

Diabetes mellitus represents a major public health threat worldwide. A serious complication of diabetes is the development of foot ulcers which, when they become infected, are the most common cause of diabetes-related hospital admissions and a leading cause of lower extremity amputation. In this review, we will update information on the diabetic foot microbiota together with the factors influencing its composition. We highlight the role of bacteria in the pathogenesis of diabetic foot ulcers. Based on current research evidence, we address the issue of differentiating infection from colonization. Finally, we emphasize the importance of the use of complementary culture and molecular-based methods for describing complex microbiotas, with a view to overcoming their respective limits.

There is currently a lack of long-term longitudinal studies investigating the stability of the microbiome. In this n-of-one study, we characterised the gut microbial composition of artist Billy Apple® from stool samples collected 45 years apart in 1970 and 2016. We observed that 45% of the microbial species were retained over the 45 year interval. Moreover, components of Apple’s microbiome associated with the allele frequency at seven SNPs in his genome. Collectively, our results are consistent with a genetic component contributing to the selection and maintenance of core members within the artist’s microbiome over his life-time.

Type-1 diabetes incidence is increasing during the last decades. Recently, a role of microbiota alteration is proposed as pre-diabetic and diabetic risk factor. A bicentric case-control study is in progress in Northern Italy. Here preliminary results are shown. The microbiome clusterization showed a division between cases and controls even if fingerprint profiles are heterogenic. Methanobrevibacter smithii is highly present only in few patients. The diversity index and the microorganism sequenced in cases and controls, seems to be quite dissimilar. The conclusive results could show a significant predictive value for the bio-indicators evaluated.

The study of the gut microbiome and virome has developed dramatically since the beginning of the 21st century. Nevertheless, giant viruses of amoebae, which are emerging viruses first described in 2003, have been largely neglected in virome investigations because they are bigger than classical viruses and devoid of ribosomal DNA. Dozens of these viruses have been isolated between 2003 and 2016, which were classified in at least 7 lineages including 2 new recognized virus families. These viruses challenge previous paradigms on viruses and share many characteristics with intra-cellular microbes. We reviewed here findings about the presence of these giant viruses of amoebae in the human gut, whose microbiota has been extensively studied during the last decade. Contrasting with what is currently done for classical viruses, many studies investigating the presence of giant viruses of amoebae have been conducted by culture on amoebae in first intention. To date, a mimivirus and a marseillevirus have been isolated from human feces, which indicates that they can still replicate after a stay in the gut. Besides, sequences related to giant viruses of amoebae have been detected in several metagenomes generated from human feces. Water is a likely source of human exposure to giant viruses of amoebae. The clinical or biological significance of the presence of these viruses in the human gut remains to be determined. Taken together, available findings warrant searching more extensively and systematically for giant viruses of amoebae in the human gut, along with in other body sites.