Human Microbiome Journal最新文献

Tetracyclines were discovered over 70 years ago and their use resulted in the emergence of tetracycline-resistance microorganisms; however, it has been hypothesized that tetracycline-resistance may have originated in the environment, and that determinants were transferred to the human gut microbiota. Ancient microbiomes represent an opportunity to explore the transmission of tetracycline-resistance determinants from the environment to humans. In the present study, tetracycline-like resistomes of three pre-Inca/Inca (10–15th centuries), and five Italian nobility (15–16th centuries) mummies were characterized using high-throughput sequencing. Sequences exhibited low homology to present-day determinants. Results may aid in the understanding of the evolution of tetracycline-resistance.

Recent studies have shown that microbe strains in normal individuals fecal microbe community are relatively stable over time. Given the role the gut microbe community plays in human health, it is important to understand if disruption of the gastrointestinal tract environment results in emergence of new genomic variants. To address this, we have used a new technique called Window-based single nucleotide similarity (WSS) to analyze the impact of several surgical procedures of the human gastrointestinal tract on the stability of the fecal microbes. Previously, we established a WSS boundary score cutoff to determine if microbe genomic variants were similar. Based on analysis of normal individuals from the Human Microbiome Project, 93% of microbes in paired fecal samples up to 1 year apart were above the cutoff, indicating similar (stable) microbes. For the current study, we analyzed fecal samples from 18 patients undergoing Roux-en-Y gastric bypass (RYGB) or 6 patients undergoing gastric sleeve for extreme obesity. From comparison of the pre-RYGB versus 1–2 year post RYGB samples from the same patients, 65% of the WSS were above the boundary cutoff, while for pre versus 1–2 year samples post surgery for patients undergoing sleeve gastrectomy, 75% of the WSS were above the cutoff. In contrast, analysis of fecal samples from 5 patients pre and post removal of segments of the sigmoid colon revealed that 97% of WSS scores were above the cutoff. Our study establishes emergence of new microbe genomic variants in the fecal community following alteration of the upper gastrointestinal environment.

Microbiome and the immune system are constantly shaping each other, in a mutual aim to thrive, defining the unstable equilibrium of the healthy individual. Microbiome is growingly involved in dysimmune conditions such as allergy, asthma, autoimmunity, and primary or acquired immune deficiencies. The current epidemics of allergic diseases and asthma has long been linked to the microbial environment through the hygiene hypothesis. Progress in the understanding of the microbiome-immune system crosstalk has unraveled a tight connection between microbial communities and the development of allergic diseases and asthma. Disruption of the microbiome affects the immune response of the host and paves the way for disease pathogenesis. Conversely, disease and therapeutic interventions affect microbial communities. We aimed at providing the reader with a view of the state-of-the art of microbiome – immune system crosstalk, with special focus on the loopholes giving potential grip to the pathogenesis of microbiome-related dysimmunity.

Uncontrolled oxidative stress has been associated with many diseases and aging. We previously report an increased gut redox and depletion of the anaerobic microbiome in severe acute malnutrition. Here, we extended the analysis to test if this link could be generalized by including individuals with various age and dietary status. Seventy individuals (children and adults, French and African, healthy individuals and teenagers with anorexia nervosa, marasmus and kwashiorkor) were included. Fecal redox potential was measured using a simple redox probe. v3v4 16S gene targeted metagenomics was used to characterize the microbiota. The Metagenomic Aerotolerant Predominance Index (MAPI) was defined as the natural logarithm of the ratio of the relative abundance of aerotolerant on strict anaerobic species. This index is easily understandable (MAPI > 0: aerotolerant predominance, MAPI < 0: anaerobic predominance), can be calculated for any metagenome and follows a normal distribution among our 70 included individuals. Fecal redox potential (mV) and the Metagenomic Aerotolerant Predominance Index were dose-dependently related (linear regression, p < .001). This link, if confirmed, will allow humans to take care of their microbiome and prevent, treat and/or alleviate gut redox associated chronic diseases by (i) controlling the concentration of reactive species in the gut by avoiding behavior associated with uncontrolled oxidative stress (alcoholism,…) in the gut and using reduced water, and (ii) by improving gut anti-oxidant capacities by an adequate diet rich in nutrients allowing the human gut to maintain a very low redox potential in the gut as a key for homeostasis.

Adult and childhood obesity rates are increasing. Childhood obesity, in particular, is a complicated, multifactorial condition that is not always explained by overeating. To address rising rates of obesity, researchers have begun to address how the composition of the gastrointestinal microbiome influences metabolism, energy absorption, and weight regulation. Colonization of the gut begins in early life and is highly influenced by method of birth (vaginal versus Caesarean), method of feeding (formula feeding versus breastfeeding), and exposure to antibiotics. Not surprisingly, an infant’s gut microbiome is very likely to resemble that of its mother. However, this means that aberrant bacteria characterized by an obese microbiome can also get passed on from an obese mom to child. To promote the colonization of a healthy infant gut microbiome, the optimal strategy generally is to have a vaginal delivery followed by exclusive breastfeeding until 6 months of age with minimal exposure to antibiotics. However, this is not always possible and overweight or obese mothers risk passing on aberrant bacteria to her children. In such cases, in conjunction with medical professionals, women can consider adding pre- and probiotics to their diets during pregnancy and lactation as well as other mitigation strategies. The colonization of an infant’s gut with optimal bacteria may help reduce the risk of obesity later in life.

Human microbiomes are complex ecosystems involving bacteria, viruses, archaea or eukaryotes that are co-evolving in an environment subject to various selective pressures, such as antibiotic administration, diet and/or lifestyle. In this sympatric lifestyle, competition is hard and the synthesis of antibiotic molecules and/or antibiotic resistance genes (ARGs) is one solution that was developed by the organisms to survive. This environment becomes a large source of ARGs for pathogenic bacteria, leading to the risk of infection due to multidrug resistant bacteria. Culture and metagenomics are two complementary methods developed to study these microbiomes in order to better understand the type of bacteria and ARGs present in the human body, as well as the factors that modulate the abundance and variety of these ARGs. The objective of this review was to identify factors that influence the colonization and propagation of multidrug resistant bacteria and/or ARGs, and to define resistance genes and multidrug resistant bacteria that have already been isolated from the human microbiota using culturomics and metagenomics techniques.

A relationship between Microbiome and its effect on depression has been suspected in earlier studies. Here we examined whether the addition of Lactobacillus probiotics which flourishes the gut-microbiota will have a beneficial adjuvant therapeutic effect on treatment of depression or even considering it as a main treatment line in the future for treatment of depression or anxiety like behavior after further studies. Mice receiving probiotics in their diet exhibited mostly similar anxiolytic and anti-depressive effects of the mice that received SSRI anti-depressant citalopram and displayed enhanced outcomes which were shown in the Tail Suspension test – which is considered a high output tool in assessing anti-depression medications –, Super oxidase dismutase concentration in the brain tissue and HPLC analysis of Kynurenine biomarker in the brain. Taken together these data support the link between healthy gut microbiome and its effect on depression-like behavior and suggest that probiotics may even have a similar therapeutic effect of anti- depressants in treatment of depression.

As a result of Next Generation Sequencing methods, metagenomic studies have become increasingly widespread. After being first applied to microbiome description, metagenomics is currently proposed as a diagnostic tool in clinical microbiology, although this application remains confined to the field of research. In this review, we will discuss the application of metagenomics to the detection of bacterial pathogens and demonstrate that the interpretation of the metagenomic results may fluctuate depending on the type of sample analyzed. However, we propose a view of metagenomic application to the evaluation of antimicrobial resistance, epidemic investigations and forensic medicine. Secondly, we present the many limits of metagenomic interpretation and application in routine clinical microbiology. From our perspective, metagenomics is not yet reliable enough for general use in clinical microbiology.

The intestinal commensal microbiota provides a myriad of benefits to the healthy host, including colonisation resistance against pathogens. Perturbations of the intestinal microbiota (dysbiosis) may adversely affect the health status of an individual and prevent protection against colonisation. The whole range of antibiotic resistance genes (resistome) in a specific microbiota is found in pathogenic and non-pathogenic bacteria. The administration of antibiotics may cause dysbiosis, contributing to the loss of colonisation resistance followed by an increment of the resistome in the intestinal microbiota. Treatments to control the current increase of multi drug-resistant (MDR) bacteria are extremely limited. In this context, the administration of healthy faecal microbiota to restore colonisation resistance and displace MDR bacteria emerges as a promising therapeutic alternative.

This brief review describes the role of the intestinal microbiota as a reservoir of MDR bacteria, the impact of different groups of antibiotics in the selection of MDR bacteria and crucially, the potential use of faecal microbiota transplantation using “healthy” or “MDR-free microbiota” to displace MDR bacteria and restore colonisation resistance.