Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun. 2009;77:2367-2375. [PMID: 19307217 DOI: 10.1128/iai.01520-08]

Pharmacomicrobiomics informs clinical pharmacogenomics

Aim: Microbiota-host-xenobiotics interactions in humans become of prime interest when clinical pharmacogenomics is to be implemented. Despite the advent of technology, information still needs to be translated into knowledge for optimum patient stratification and disease management. Material & methods: Herein, we mined metagenomic, pharmacometagenomic and pharmacomicrobiomic datasets to map microbiota-host-drugs networks. Results: Datasets were multifaceted and voluminous. Interoperability, data sparsity and scarcity remain a challenge. Mapping microbiota-host-drugs networks allowed the prediction of drug response/toxicity and modulation of the microbiota-host-drugs interplay. Conclusion: Our approach triangulated microbiota, host and drug networks revealing the need for contextual data and open science via microattribution to accelerate knowledge growth. Our findings may serve as a data storehouse for a user-friendly query system, coupled with databanks and databases.

Modeling the temporal dynamics of the gut microbial community in adults and infants

Given the highly dynamic and complex nature of the human gut microbial community, the ability to identify and predict time-dependent compositional patterns of microbes is crucial to our understanding of the structure and functions of this ecosystem. One factor that could affect such time-dependent patterns is microbial interactions, wherein community composition at a given time point affects the microbial composition at a later time point. However, the field has not yet settled on the degree of this effect. Specifically, it has been recently suggested that only a minority of taxa depend on the microbial composition in earlier times. To address the issue of identifying and predicting temporal microbial patterns we developed a new model, MTV-LMM (Microbial Temporal Variability Linear Mixed Model), a linear mixed model for the prediction of microbial community temporal dynamics. MTV-LMM can identify time-dependent microbes (i.e., microbes whose abundance can be predicted based on the previous microbial composition) in longitudinal studies, which can then be used to analyze the trajectory of the microbiome over time. We evaluated the performance of MTV-LMM on real and synthetic time series datasets, and found that MTV-LMM outperforms commonly used methods for microbiome time series modeling. Particularly, we demonstrate that the effect of the microbial composition in previous time points on the abundance of taxa at later time points is underestimated by a factor of at least 10 when applying previous approaches. Using MTV-LMM, we demonstrate that a considerable portion of the human gut microbiome, both in infants and adults, has a significant time-dependent component that can be predicted based on microbiome composition in earlier time points. This suggests that microbiome composition at a given time point is a major factor in defining future microbiome composition and that this phenomenon is considerably more common than previously reported for the human gut microbiome.

The ability to characterize and predict temporal trajectories of the microbial community in the human gut is crucial to our understanding of the structure and functions of this ecosystem. In this study we develop MTV-LMM, a method for modeling time-series microbial community data. Using MTV-LMM we find that in contrast to previous reports, a considerable portion of microbial taxa in both infants and adults display temporal structure that is predictable using the previous composition of the microbial community. In reaching this conclusion we have adopted a number of concepts common in statistical genetics for use with longitudinal microbiome studies. We introduce concepts such as time-explainability and the temporal kinship matrix, which we believe will be of use to other researchers studying microbial dynamics, through the framework of linear mixed models. In particular we find that the association matrix estimated by MTV-LMM reveals known phylogenetic relationships and that the temporal kinship matrix uncovers known temporal structure in infant microbiome and inter-individual differences in adult microbiome. Finally, we demonstrate that MTV-LMM significantly outperforms commonly used methods for temporal modeling of the microbiome, both in terms of its prediction accuracy as well as in its ability to identify time-dependent taxa.

Modified Mouse Model of Clostridioides difficile Infection as a Platform for Probiotic Efficacy Studies

Probiotics may represent a promising approach for reducing Clostridioides (Clostridium) difficile infections (CDIs). A clinical trial conducted by our group demonstrated that CDI patients undergoing adjunctive treatment with Lactobacillus and Bifidobacterium probiotics had a reduction in diarrheal duration and compositional changes in their stool microbiomes. Here, we modified a CDI mouse model to represent clinical outcomes observed in patients and employed this model to identify evidence for the prevention of primary CDI and relapse with the same probiotic. Mice (n = 80) were administered 0.25 mg/ml cefoperazone over 5 days and subsequently challenged with 10² C. difficile VPI 10463 spores. A subset of mice (n = 40) were administered 10⁸ CFU of probiotics daily alongside cefoperazone pretreatment and until experimental endpoints were reached. Clinical scoring was performed daily on mice and used to evaluate CDI onset and severity. Moderate CDI in mice was defined by survival beyond day 3 postinfection, while mice with severe CDI were those who succumbed to infection prior to day 3 postinfection. Sequencing and analysis of 16S rRNA from stool content were performed to determine compositional alterations to the microbiota. Using total clinical scores, we identified an association between probiotic treatment and delayed onset of primary CDI and relapse by approximately 12 to 24 h (P < 0.001). The stool microbiome of mice with moderate CDI receiving probiotic treatment was significantly enriched with Lachnospiraceae during primary CDI (P < 0.05). The outcomes observed present an opportunity to use this modified CDI mouse model to examine the efficacy of nonantibiotic options for CDI management.

Rethinking antimicrobial stewardship paradigms in the context of the gut microbiome

Ongoing concerns over the presence and persistence of antimicrobial resistance (AMR), particularly in Gram-negative bacteria, continue to have significant global health impacts. The gastrointestinal tract, or 'gut', environment amplifies AMR in the human gut microbiome, even in the absence of antibiotics. It constitutes a complex and diverse community of organisms, and patterns and alterations within it are increasingly being found to be associated with states of health and disease. Our understanding of the effects of routes of administration of antimicrobials on the gut microbiome is still lacking despite recent advances in metagenomics. In this article we review current evidence for antibiotic effects on gut microbiota and explore possible prescribing and stewardship approaches that would seek to minimize these effects. If we are to preserve existing and new antimicrobials, we need to consider their use in the context of their effect on gut ecology, and the human microbiome in general.

Antimicrobial Effects on Swine Gastrointestinal Microbiota and Their Accompanying Antibiotic Resistome

Antimicrobials are the most commonly prescribed drugs in the swine industry. While antimicrobials are an effective treatment for serious bacterial infections, their use has been associated with major adverse effects on health. It has been shown that antimicrobials have substantial direct and indirect impacts on the swine gastrointestinal (GI) microbiota and their accompanying antimicrobial resistome. Antimicrobials have also been associated with a significant public health concern through selection of resistant opportunistic pathogens and increased emergence of antimicrobial resistance genes (ARGs). Since the mutualistic microbiota play a crucial role in host immune regulation and in providing colonization resistance against potential pathogens, the detrimental impacts of antimicrobial treatment on the microbiota structure and its metabolic activity may lead to further health complications later in life. In this review, we present an overview of antimicrobial use in the swine industry and their role in the emergence of antimicrobial resistance. Additionally, we review our current understanding of GI microbiota and their role in swine health. Finally, we investigate the effects of antimicrobial administration on the swine GI microbiota and their accompanying antibiotic resistome. The presented data is crucial for the development of robust non-antibiotic alternative strategies to restore the GI microbiota functionality and guarantee effective continued use of antimicrobials in the livestock production system.

Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach

Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.

Bacteriophage versus antibiotic therapy on gut bacterial communities of juvenile green turtle, Chelonia mydas

Green turtles are endangered marine herbivorous hindgut fermenters that contribute to a variety of marine ecosystems. Debilitated turtles are often rehabilitated in turtle hospitals. Since accurate diagnosis of disease is difficult, broad-spectrum antibiotics are routinely used as a general treatment, potentially causing collateral damage to the gut microbiome of the patient. Here, we evaluated the concept of the application of bacteriophage (phages) to eliminate targeted intestinal bacteria as an alternative to a broad-spectrum antibiotic (enrofloxacin) in clinically healthy, captive green turtles. Additionally, the impact of a broad-spectrum antibiotic (enrofloxacin) and phage therapy on the gut bacterial communities of green turtles was evaluated. Gut bacterial communities in faecal samples were analysed by sequencing the V1-V3 regions of the bacterial 16S rRNA. Bacteria-specific phage cocktails significantly (P < 0.05) reduced targeted Acinetobacter in phage-treated turtles during the therapy. Compared to control, no significant difference was observed in the bacterial diversity and compositions in phage-treated turtles. In contrast, bacterial diversity was significantly (P < 0.05) reduced in antibiotic-treated turtles at day 15 and throughout the trial. The alteration in the bacterial microbiota of antibiotic-treated turtles was largely due to an increase in abundance of Gram-positive Firmicutes and a concurrent decrease in Gram-negative Bacteroidetes, Proteobacteria and Verrucomicrobia. Additionally, we observed the relative abundance of several bacteria at lower taxonomic level was much less affected by phages than by antibiotics. These data offer the proof of concept of phage therapy to manipulate transient as well as indigenous bacterial flora in gut-related dysbiosis of turtles.

The Cutaneous Microbiome: Implications for Dermatology Practice

The human integument is inhabited by a vast array of microorganisms known collectively as the cutaneous microbiome. As a result of advances in laboratory science, our understanding of the diversity and complexity of the human microbiome is rapidly evolving. In particular, advances in the field of genomics have enabled the study of the cutaneous microbiome with a hitherto unimaginable level of detail, resulting in a maturation of our understanding of cutaneous health and disease. Herein, we review current microbiology concepts and highlight the key features of recent laboratory advances, particularly with respect to genomics. We provide a summary of new findings related to normal skin flora, interactions between host immunity and microbial communities, and microbial relationships with common skin disorders. Finally, we review the implications for dermatologists.

Understanding regeneration at different scales

Regeneration occurs at many different levels in nature, from individual organisms (notably earthworms and hydra), through communities of microbes, to ecosystems such as forests. Researchers in the life sciences and the history and philosophy of science are collaborating to explore how the processes of repair and recovery observed at these different scales are related.

Association between extrauterine growth restriction and changes of intestinal flora in Chinese preterm infants

The aim of the study was to investigate any association between extrauterine growth restriction (EUGR) and intestinal flora of <30-week-old preterm infants. A total of 59 preterm infants were assigned to EUGR (n=23) and non-EUGR (n=36) groups. Intestinal bacteria were compared by using high-throughput sequencing of bacterial rRNA. The total abundance of bacteria in 344 genera (7568 v. 13,760; P<0.0001) and 456 species (10,032 v. 18,240; P<0.0001) was significantly decreased in the EUGR group compared with the non-EUGR group. After application of a multivariate logistic model and adjusting for potential confounding factors, as well as false-discovery rate corrections, we found four bacterial genera with higher and one bacterial genus with lower abundance in the EUGR group compared with the control group. In addition, the EUGR group showed significantly increased abundances of six species (Streptococcus parasanguinis, Bacterium RB5FF6, two Klebsiella species and Microbacterium), but decreased frequencies of three species (one Acinetobacter species, Endosymbiont_of_Sphenophorus_lev and one Enterobacter_species) compared with the non-EUGR group. Taken together, there were significant changes in the intestinal microflora of preterm infants with EUGR compared to preterm infants without EUGR.

Thirty Years of Lactobacillus rhamnosus GG: A Review

Lactobacillus rhamnosus GG (LGG) was the first strain belonging to the genus Lactobacillus to be patented in 1989 thanks to its ability to survive and to proliferate at gastric acid pH and in medium containing bile, and to adhere to enterocytes. Furthermore LGG is able to produces both a biofilm that can mechanically protect the mucosa, and different soluble factors beneficial to the gut by enhancing intestinal crypt survival, diminishing apoptosis of the intestinal epithelium, and preserving cytoskeletal integrity. Moreover LGG thanks to its lectin-like protein 1 and 2 inhibits some pathogens such as Salmonella species. Finally LGG is able to promote type 1 immune-responsiveness by reducing the expression of several activation and inflammation markers on monocytes and by increasing the production of interleukin-10, interleukin-12 and tumor necrosis factor-α in macrophages. A large number of research data on Lactobacillus GG is the basis for the use of this probiotic for human health. In this review we have considered predominantly randomized controlled trials, meta-analysis, Cochrane Review, guide lines of Scientific Societies and anyway studies whose results were evaluated by means of relative risk, odds ratio, weighted mean difference 95% confidence interval. The effectiveness of LGG in gastrointestinal infections and diarrhea, antibiotic and Clostridium difficile associated diarrhea, irritable bowel syndrome, inflammatory bowel disease, respiratory tract infections, allergy, cardiovascular diseases, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis, cystic fibrosis, cancer, elderly end sport were analyzed.

Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota

Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota and reduce competition for available nutrients, resulting in imbalance among commensal species and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of C. difficile with commensal species from the three dominant phyla in the human gut, we developed a multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile, Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance. We tuned the model to produce species abundances and short-chain fatty acid levels consistent with available data for healthy individuals. The model predicted that experimentally-observed host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels and/or increased primary bile acid levels would induce large increases in C. difficile abundance and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation of increased host nitrate secretion, the model also was able to predict increased E. coli abundance associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient levels and disease progression, the model generated hypotheses for future testing and has the capability to support the development of new treatment strategies for C. difficile gut infections.

The difference in nasal bacterial microbiome diversity between chronic rhinosinusitis patients with polyps and a control population

BACKGROUND

Little is known regarding the role of the microbiome of the paranasal sinuses and its contribution to sinus mucosal health and disease. Consequently, we examined the microbiome of chronic rhinosinusitis patients with polyps (CRSwNP) and a control population to provide new insights into the microbiota associated with the pathogenesis of CRSwNP.

METHODS

Fifty-nine CRSwNP patients and 27 controls were enrolled in the study. The bacterial communities of the middle meatus were detected using 16S ribosomal RNA (rRNA)-targeted Illumina MiSeq sequencing after microbial DNA was extracted from swabs.

RESULTS

Although there was no difference in diversity between the 2 groups, richness was lower in the CRSwNP group than in the control group (p = 0.03). At the phylum level, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were predominant in both groups; however, the relative abundance was different, with the proportions of Actinobacteria (predominantly Corynebacterium) and Dolosigranulum being significantly higher in the control group than in the CRSwNP group.

CONCLUSION

These results support the theory of microbial dysbiosis as the pathogenesis of CRSwNP. The reduction in the proportions of potentially protective bacteria may decrease the overall stability of the sinonasal bacterial community.

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs

Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs (P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia-Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome.

Ultraviolet radiation, both UVA and UVB, influences the composition of the skin microbiome

BACKGROUND

Studies have begun to investigate the complex relationship between host and microorganisms in non-infectious pathologies such as acne, atopic dermatitis and psoriasis. Though the skin is exposed to environmental stressors such as ultraviolet radiation (UVR), no studies exist examining the effects of both UVA and UVB on the skin microbiome.

OBJECTIVE

To test the effect of UVA and UVB on human skin microbiome.

METHODS

To test whether UV will alter the cutaneous microbiome, participants were exposed to doses of UVA (22-47 J/cm² ) or UVB (100-350 mJ/cm² ) and samples were collected. DNA was isolated and sequenced to identify the microbial composition of each sample.

RESULTS

There was vast intra- and inter-subject variation at all time points, and phylum and species-level differences were identified. These included an increase in the phylum Cyanobacteria and a decrease in the family Lactobacillaceae and Pseudomonadaceae. The sensitivity of microbes to UVR and their re-colonization potential following exposure differed in UVA vs UVB samples.

LIMITATIONS

The sample size was small, and the study was limited to males.

CONCLUSION

The results demonstrate that UVR has profound qualitative and quantitative influences on the composition of the skin microbiome, possibly effecting skin pathology in which UVR is a factor.

The gut microbiome is required for full protection against acute arsenic toxicity in mouse models

Arsenic poisons an estimated 200 million people worldwide through contaminated food and drinking water. Confusingly, the gut microbiome has been suggested to both mitigate and exacerbate arsenic toxicity. Here, we show that the microbiome protects mice from arsenic-induced mortality. Both antibiotic-treated and germ-free mice excrete less arsenic in stool and accumulate more arsenic in organs compared to control mice. Mice lacking the primary arsenic detoxification enzyme (As3mt) are hypersensitive to arsenic after antibiotic treatment or when derived germ-free, compared to wild-type and/or conventional counterparts. Human microbiome (stool) transplants protect germ-free As3mt-KO mice from arsenic-induced mortality, but protection depends on microbiome stability and the presence of specific bacteria, including Faecalibacterium. Our results demonstrate that both a functional As3mt and specific microbiome members are required for protection against acute arsenic toxicity in mouse models. We anticipate that the gut microbiome will become an important explanatory factor of disease (arsenicosis) penetrance in humans, and a novel target for prevention and treatment strategies.

It is unclear whether the gut microbiome can mitigate or exacerbate arsenic toxicity. Here, Coryell et al. show that the human gut microbiome protects mice from arsenic-induced mortality, with protection levels correlating with the relative abundance of the human commensal Faecalibacterium.

Antibiotics in early life: dysbiosis and the damage done

Antibiotics are the most common type of medication prescribed to children, including infants, in the Western world. While use of antibiotics has transformed previously lethal infections into relatively minor diseases, antibiotic treatments can have adverse effects as well. It has been shown in children, adults and animal models that antibiotics dramatically alter the gut microbial composition. Since the gut microbiota plays crucial roles in immunity, metabolism and endocrinology, the effects of antibiotics on the microbiota may lead to further health complications. In this review, we present an overview of the effects of antibiotics on the microbiome in children, and correlate them to long-lasting complications of obesity, behavior, allergies, autoimmunity and other diseases.

Effects of Early Intervention with Maternal Fecal Microbiota and Antibiotics on the Gut Microbiota and Metabolite Profiles of Piglets

We investigated the effects of early intervention with maternal fecal microbiota and antibiotics on gut microbiota and the metabolites. Five litters of healthy neonatal piglets (Duroc × Landrace × Yorkshire, nine piglets in each litter) were used. Piglets in each litter were orally treated with saline (CO), amoxicillin treatment (AM), or maternal fecal microbiota transplantation (MFMT) on days 1–6, with three piglets in each treatment. Results were compared to the CO group. MFMT decreased the relative abundances of Clostridium sensu stricto and Parabacteroides in the colon on day 7, whereas the abundance of Blautia increased, and the abundance of Corynebacterium in the stomach reduced on day 21. AM reduced the abundance of Arcanobacterium in the stomach on day 7 and reduced the abundances of Streptococcus and Lachnoclostridium in the ileum and colon on day 21, respectively. The metabolite profile indicated that MFMT markedly influenced carbohydrate metabolism and amino acid (AA) metabolism on day 7. On day 21, carbohydrate metabolism and AA metabolism were affected by AM. The results suggest that MFMT and AM discriminatively modulate gastrointestinal microflora and alter the colonic metabolic profiles of piglets and show different effects in the long-term. MFMT showed a location-specific influence on the gastrointestinal microbiota.

Antibiotics and autoimmune and allergy diseases: Causative factor or treatment?

The newborn infant emerges from an almost sterile environment into a world of bacteria. Bacteria colonize the infant's skin, lungs, and, of most importance, the gut. The process of bacterial colonization is coordinated, and each body niche acquires a unique composition of bacteria. In the gut, most bacteria belong to the Firmicutes and Bacteroidetes phyla, while Actinobacteria and Proteobacteria are far less abundant. Some of these bacteria possess strong immunoregulatory properties. Bacterial colonization is essential to skew the newborn's immune response away from the allergy-favoring Type-2 response towards a Type-1 immune response, which is essential for pathogen elimination. Imbalance between Type 1 and Type 2 responses, however, can promote autoimmunity. In addition, the microbiota shapes immune responses in adults. Autoimmune and allergic diseases are commonly associated with an altered composition of resident bacteria, which is known as dysbiosis. Perhaps the most common cause of disruption and alteration of the bacterial colonization of newborns is the use of antibiotics. It is not known whether the dysbiosis precedes or is the consequence of allergic and autoimmune disorders, and whether antibiotics can be a trigger for these disorders, depending on the type of antibiotic used and the maturity of immune system. In this review, we discuss the development of the microbiota in different body niches and their immunomodulatory potential. We evaluate the impact of antibiotics, both in mice and in humans, on microbial communities and how that may impact the development and manifestation of diseases through all stages of life: the prenatal period, childhood, and adulthood.

Postnatal Administration of Lactobacillus rhamnosus HN001 Ameliorates Perinatal Broad-Spectrum Antibiotic-Induced Reduction in Myelopoiesis and T Cell Activation in Mouse Pups

SCOPE

This study addresses whether administration of Lactobacillus rhamnosus HN001 could mitigate the effects of a compromised gut microbiota on the composition of mature leukocytes and granulocyte-macrophage progenitor cells (GMPs) in newborn mice.

METHODS AND RESULTS

Pregnant dams receive oral broad-spectrum antibiotics, which dramatically decrease the gut microbial composition analyzed by 16S rRNA sequencing. Perinatal antibiotic treatment decreases the proportions of bone marrow (BM) GMPs (postnatal day (PND2): 0.5% vs 0.8%, PND4: 0.2% to 0.6%) and mature granulocytes (33% vs 24% at PND2), and spleen granulocytes (7% vs 17% at PND2) and B cells (PND2:18% vs 28%, PND4:11% vs 22%). At PND35, T helper (Th) cells (20% vs 14%) and cytotoxic T (Tc) cells (10% vs 8%) decrease in the spleen. Oral administration of L. rhamnosus HN001 to neonatal pups (PND1-7) restores the antibiotic-induced changes of GMPs and granulocytes in BM and spleen, and further increases splenic granulocytes in control pups. At PND35, splenic proportions of B and Th but not Tc cells are restored.

CONCLUSION

Postnatal administration of a single bacterial strain efficiently restores granulopoiesis and most T cell activation in neonatal mice that suffer from a perinatal antibiotic-induced compromised gut microbiota at birth.

Changes in Gut Microbiota Prior to Influenza A Virus Infection Do Not Affect Immune Responses in Pups or Juvenile Mice

Previous studies demonstrated that oral antibiotic (ABX) treatment prior to and during influenza A virus (IAV) infection of adult mice profoundly altered gut microbiota (GM) and was associated with increased susceptibility and impaired immunity to IAV. We examined the impact of ABX during critical times relevant to the establishment of GM in early life (using perinatal treatment of neonates and direct treatment of juvenile mice) and asked whether cessation of ABX treatment in early life had lasting effects on GM composition and anti-IAV immunity. ABX treatment significantly changed GM composition in juvenile mice and in ABX-treated dams. However, if ABX treatment ceased at the time of infection, neither neonates nor juvenile mice showed enhanced susceptibility to IAV, nor were major differences detected in cellular and humoral adaptive antiviral immunity. Thus, while ABX treatment alters GM diversity in early life, cessation and subsequent re-colonization correlates with effective immunity against IAV.

The Human Gut Microbiome - A Potential Controller of Wellness and Disease

Interest toward the human microbiome, particularly gut microbiome has flourished in recent decades owing to the rapidly advancing sequence-based screening and humanized gnotobiotic model in interrogating the dynamic operations of commensal microbiota. Although this field is still at a very preliminary stage, whereby the functional properties of the complex gut microbiome remain less understood, several promising findings have been documented and exhibit great potential toward revolutionizing disease etiology and medical treatments. In this review, the interactions between gut microbiota and the host have been focused on, to provide an overview of the role of gut microbiota and their unique metabolites in conferring host protection against invading pathogen, regulation of diverse host physiological functions including metabolism, development and homeostasis of immunity and the nervous system. We elaborate on how gut microbial imbalance (dysbiosis) may lead to dysfunction of host machineries, thereby contributing to pathogenesis and/or progression toward a broad spectrum of diseases. Some of the most notable diseases namely Clostridium difficile infection (infectious disease), inflammatory bowel disease (intestinal immune-mediated disease), celiac disease (multisystemic autoimmune disorder), obesity (metabolic disease), colorectal cancer, and autism spectrum disorder (neuropsychiatric disorder) have been discussed and delineated along with recent findings. Novel therapies derived from microbiome studies such as fecal microbiota transplantation, probiotic and prebiotics to target associated diseases have been reviewed to introduce the idea of how certain disease symptoms can be ameliorated through dysbiosis correction, thus revealing a new scientific approach toward disease treatment. Toward the end of this review, several research gaps and limitations have been described along with suggested future studies to overcome the current research lacunae. Despite the ongoing debate on whether gut microbiome plays a role in the above-mentioned diseases, we have in this review, gathered evidence showing a potentially far more complex link beyond the unidirectional cause-and-effect relationship between them.

Lactobacillus salivarius reverse antibiotic-induced lung defense impairment in a ventilator model

Background

Widespread use of antibiotics in the intensive care unit is a potential cause of the emergence of hospital-acquired pneumonia. This study determined whether Lactobacillus salivarius feeding could reverse antibiotic-induced lung defense impairment in a ventilator model.

Methods

C57BL/6 wild-type (WT) mice received mechanical ventilation for 3 h after intramuscular antibiotic treatment for 6 days. Treatment with dead Lactobacillus salivarius and fructo-oligosaccharides (FOS) feeding were used to stimulate antibacterial protein expression in the intestine. Reactive oxygen species (ROS) in the intestinal mucosa was detected using 2ʹ7ʹ-dichlorofluorescein diacetate. The peroxynitrite production of alveolar macrophages (AMs) was measured using dihydrorhodamine 123 oxidation assay. N-acetylcysteine (NAC), an ROS scavenger, was orally administered to mice receiving antibiotics with FOS feeding.

Results

Antibiotic treatment decreased Pseudomonas aeruginosa (PA) phagocytic activity and activity of AMs and protein expression of regenerating islet-derived protein 3β (Reg3β) as well as Toll-like receptor 4 (TLR4) in the intestinal mucosa in the ventilator model. Antibiotic treatment also decreased ROS production in the intestinal mucosa, peroxynitrite production of AMs, and RELMβ expression as well as NF-κB DNA binding activity of the intestinal mucosa in WT mice but not in MyD88^−/− mice. Treatment with dead L. salivarius or FOS feeding increased ROS production, bacterial killing activity, and protein expression of Reg3β as well as TLR4 in the intestinal mucosa and reversed the inhibitory effects of antibiotics on PA phagocytic activity of AMs.

Conclusion

Taken together with the finding that ablation of FOS-induced intestinal ROS using NAC decreased peroxynitrite production as well as PA phagocytic activity of AMs and protein expression of CRP-ductin, IL-17, Reg3β, and RELMβ in the intestinal mucosa, we conclude that commensal microflora plays a key role in stimulating lung immunity. Intestinal ROS plays a role as a predictive indicator and modulator of pulmonary defense mechanisms. Antibiotic treatment reduces lung defense against PA infection through the decrease in intestinal Reg3β and TLR4 expression. Treatment with dead L. salivarius or FOS feeding reverses the antibiotic-induced lung defense impairment through the intestinal ROS/MyD88 pathways.

Drug-mediated metabolic tipping between antibiotic resistant states in a mixed-species community

Microbes rarely exist in isolation, rather, they form intricate multi-species communities that colonize our bodies and inserted medical devices. However, the efficacy of antimicrobials is measured in clinical laboratories exclusively using microbial monocultures. Here, to determine how multi-species interactions mediate selection for resistance during antibiotic treatment, particularly following drug withdrawal, we study a laboratory community consisting of two microbial pathogens. Single-species dose responses are a poor predictor of community dynamics during treatment so, to better understand those dynamics, we introduce the concept of a dose-response mosaic, a multi-dimensional map that indicates how species' abundance is affected by changes in abiotic conditions. We study the dose-response mosaic of a two-species community with a 'Gene × Gene × Environment × Environment' ecological interaction whereby Candida glabrata, which is resistant to the antifungal drug fluconazole, competes for survival with Candida albicans, which is susceptible to fluconazole. The mosaic comprises several zones that delineate abiotic conditions where each species dominates. Zones are separated by loci of bifurcations and tipping points that identify what environmental changes can trigger the loss of either species. Observations of the laboratory communities corroborated theory, showing that changes in both antibiotic concentration and nutrient availability can push populations beyond tipping points, thus creating irreversible shifts in community composition from drug-sensitive to drug-resistant species. This has an important consequence: resistant species can increase in frequency even if an antibiotic is withdrawn because, unwittingly, a tipping point was passed during treatment.

Use of a combination of in vitro models to investigate the impact of chlorpyrifos and inulin on the intestinal microbiota and the permeability of the intestinal mucosa

Dietary exposure to the organophosphorothionate pesticide chlorpyrifos (CPF) has been linked to dysbiosis of the gut microbiota. We therefore sought to investigate whether (i) CPF's impact extends to the intestinal barrier and (ii) the prebiotic inulin could prevent such an effect. In vitro models mimicking the intestinal environment (the SHIME®) and the intestinal mucosa (Caco-2/TC7 cells) were exposed to CPF. After the SHIME® had been exposed to CPF and/or inulin, we assessed the system's bacterial and metabolic profiles. Extracts from the SHIME®'s colon reactors were then transferred to Caco-2/TC7 cultures, and epithelial barrier integrity and function were assessed. We found that inulin co-treatment partially reversed CPF-induced dysbiosis and increased short-chain fatty acid production in the SHIME®. Furthermore, co-treatment impacted tight junction gene expression and inhibited pro-inflammatory signaling in the Caco-2/TC7 intestinal cell line. Whereas, an isolated in vitro assessment of CPF and inulin effects provides useful information on the mechanism of dysbiosis, combining two in vitro models increases the in vivo relevance.

Exposure to nanoplastics disturbs the gut microbiome in the soil oligochaete Enchytraeus crypticus

Microplastics are emerging pollutants that have recently aroused considerable concern but most toxicological studies have focused on marine biota, with little investigation of the influence of microplastics on terrestrial ecosystems. Here, we fed the soil oligochaete Enchytraeus crypticus with oatmeal containing 0, 0.025, 0.5, and 10% (dry weight basis) nano-polystyrene (0.05-0.1 μm particle size) to elucidate the impact of microplastics on the growth and gut microbiome of Enchytraeus crypticus. We observed a significant reduction of weight in the animals fed 10% polystyrene and an increase in the reproduction of those fed 0.025%. More importantly, using 16S rRNA amplification and high-throughput sequencing we found a significant shift in the microbiome of those fed 10% microplastics with significant decreases in the relative abundance of the families Rhizobiaceae, Xanthobacteraceae and Isosphaeraceae. These families contain key microbes that contribute to nitrogen cycling and organic matter decomposition.

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model

Despite the tremendous biological activity of polysaccharides from the mushroom Dictyophora indusiata, its role in the restoration of gut microbiota has not yet been explored. The present study aimed to investigate whether D. indusiata polysaccharide (DIP) could modulate the recovery of gut microbiota composition and intestinal barrier function after broad-spectrum antibiotic-driven dysbiosis. Alteration and restoration in the microbial communities were elucidated by the Illumina MiSeq platform. Colon histology, expression of tight-junction associated proteins, and serum/tissue endotoxin and cytokine levels were evaluated. Two-week daily oral administration of clindamycin and metronidazole resulted in reduced bacterial diversity and richness, and perturbed the microbial flora at various taxonomic levels (altered Firmicutes/Bacteroidetes ratio and increased relative abundance of harmful flora (Proteobacteria, Enterococcus, and Bacteroides)), whereas DIP administration reversed the dysbiosis and increased beneficial flora, including Lactobacillaceae (lactic acid-producing bacteria), and Ruminococaceae (butyrate-producing bacteria). In addition, it resulted in the reduction of endotoxemia (through lipopolysaccharides (LPSs)) and pro-inflammatory cytokine (tumor necrosis factor alpha (TNF-α), interleukin 6 (IL-6), and interleukin 1β (IL-1β)) levels, with the increased expression of tight-junction associated proteins (claudin-1, occludin, and zonula occludens-1). These findings not only suggested a comprehensive understanding of the protective effects of a DIP in the restoration of gut microbiota but also highlighted its role in the enhancement of gut barrier integrity, reduction of inflammation and lowering of endotoxin levels in mice.

Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients

This study examines the impact of cefepime and APP-β (antipseudomonal penicillin/ β-lactamase inhibitor combinations) on Gram-negative bacterial colonization and resistance in two Australian ICUs. While resistance did not cumulatively increase, cefepime (but not APP-β treatment) was associated with acquisition of antibiotic resistant Enterobacteriaceae, consistent with an ecological effect. Analysis of the resident gut E. coli population in a subset of patients showed an increase in markers of horizontal gene transfer after cefepime exposure that helps explain the increase in APP-β resistance and reminds us that unmeasured impacts on the microbiome are key outcome determinants that need to be fully explored.

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults

Clinical effects of antimicrobials and probiotics in combination have been reported, however, little is known about their impact on gut microbiota and its resistome. In this study 16S rRNA gene amplicon, shotgun metagenomics sequencing and antibiotic resistance (ABR) microarray were used on fecal samples of 70 healthy participants, taken at four time points in probiotic (Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052) and placebo groups to profile the gut bacterial microbiota and its resistome following administration of amoxicillin-clavulanic acid for one week. Significant shifts in microbiota family composition caused by the antimicrobial in both groups that included decreases in the proportion of Lachnospiraceae, Coriobacteriaceae and unidentified Clostridiales; and notable increases for the proportion of Enterobacteriaceae, Bacteroidaceae and Porphyromonadaceae compared to baseline levels. Resistome showed a corresponding enrichment of ABR genes compared to baseline from such classes as aminoglycosides and beta-lactams that were linked, by in silico inference, to the enrichment of the family Enterobacteriaceae. Despite perturbations caused by short-term antibiotic treatment, both gut microbiota and resistome showed prompt recovery to baseline levels one week after cessation of the antimicrobial. This rapid recovery may be explained by the hypothesis of community resilience.

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization

Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may "attack the loser" in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration.

The gut is home to a large and diverse community of bacteria and other microbes, known as the gut microbiota. The makeup of this community is important for the health of both the host and its residents. For instance, many gut bacteria help to digest food or keep disease-causing bacteria in check. In return, the host provides them with nutrients. When this balance is disturbed, the host is exposed to risks such as infections. In particular, treatments with antibiotics that kill gut bacteria can lead to side effects like diarrhea, because the gut becomes recolonized with harmful bacteria including Clostridium difficile and Salmonella.

Reese et al. have now investigated what happens to the gut environment after antibiotic treatment and how the gut microbiota recovers. Mice treated with broad-spectrum antibiotics showed an increase in the “redox potential” of their gut environment. Redox potential captures a number of measures of the chemical makeup of an environment, and provides an estimate for how efficiently some bacteria in that environment can grow. Some of the change in redox potential came from the host’s own immune system releasing chemicals as it reacted to the effects of the treatment. However, Reese et al. found that treating gut bacteria in an artificial gut – which has no immune system – also increased the redox potential. This experiment suggests that bacteria actively shape their chemical environment in the gut.

After the treatment, bacteria that thrive under high redox potentials, which include some disease-causing species, recovered first and fastest. This, in turn, helped to bring redox potential back to how it was before the treatment. Although the gut’s chemical environment recovered, some bacterial species were wiped out by the antibiotic treatment. The microbiota only returned to its previous state when the treated mice were housed together with non-treated mice. This was expected because mice that live together commonly exchange microbes, for instance by eating each other’s feces, and the treated mice received new species to replenish their microbiota.

These findings are important because they show that the chemical environment shapes and is shaped by the bacterial communities in the gut. Future research may investigate if altering redox potential in the gut could help to keep the microbiota healthier in infections and diseases of the digestive tract.

Host genetics and microbiome associations through the lens of genome wide association studies

Recent studies indicate that the gut microbiome is partially heritable, motivating the need to investigate microbiome-host genome associations via microbial genome-wide association studies (mGWAS). Existing mGWAS demonstrate that microbiome-host genotype associations are typically weak and are spread across multiple variants, similar to associations often observed in genome-wide association studies (GWAS) of complex traits. Here we reconsider mGWAS by viewing them through the lens of GWAS, and demonstrate that there are striking similarities between the challenges and pitfalls faced by the two study designs. We further advocate the mGWAS community to adopt three key lessons learned over the history of GWAS: firstly, adopting uniform data and reporting formats to facilitate replication and meta-analysis efforts; secondly, enforcing stringent statistical criteria to reduce the number of false positive findings; and thirdly, considering the microbiome and the host genome as distinct entities, rather than studying different taxa and single nucleotide polymorphism (SNPs) separately. Finally, we anticipate that mGWAS sample sizes will have to increase by orders of magnitude to reproducibly associate the host genome with the gut microbiome.

Clostridium difficile - From Colonization to Infection

Clostridium difficile is the most frequent cause of nosocomial antibiotic-associated diarrhea. The incidence of C. difficile infection (CDI) has been rising worldwide with subsequent increases in morbidity, mortality, and health care costs. Asymptomatic colonization with C. difficile is common and a high prevalence has been found in specific cohorts, e.g., hospitalized patients, adults in nursing homes and in infants. However, the risk of infection with C. difficile differs significantly between these cohorts. While CDI is a clear indication for therapy, colonization with C. difficile is not believed to be a direct precursor for CDI and therefore does not require treatment. Antibiotic therapy causes alterations of the intestinal microbial composition, enabling C. difficile colonization and consecutive toxin production leading to disruption of the colonic epithelial cells. Clinical symptoms of CDI range from mild diarrhea to potentially life-threatening conditions like pseudomembranous colitis or toxic megacolon. While antibiotics are still the treatment of choice for CDI, new therapies have emerged in recent years such as antibodies against C. difficile toxin B and fecal microbial transfer (FMT). This specific therapy for CDI underscores the role of the indigenous bacterial composition in the prevention of the disease in healthy individuals and its role in the pathogenesis after alteration by antibiotic treatment. In addition to the pathogenesis of CDI, this review focuses on the colonization of C. difficile in the human gut and factors promoting CDI.

Fecal Microbiota Transplantation: Therapeutic Potential for a Multitude of Diseases beyond Clostridium difficile

The human intestinal tract contains trillions of bacteria, collectively called the gut microbiota. Recent insights have linked the gut microbiota to a plethora of diseases, including Clostridium difficile infection (CDI), inflammatory bowel disease (IBD), and metabolic diseases such as obesity, type 2 diabetes (T2D), and nonalcoholic steatohepatitis (NASH). Fecal microbiota transplantation (FMT) is currently tested as a therapeutic option in various diseases and can also help to dissect association from causality with respect to gut microbiota and disease. In CDI, FMT has been shown to be superior to antibiotic treatment. For IBD, T2D, and NASH, several placebo-controlled randomized controlled trials are under way. Moreover, techniques and standardization are developing. With the extension of FMT as a treatment modality in diseases other than CDI, a whole new treatment option may be emerging. Moreover, correlating alterations in specific strains to disease outcome may prove pivotal in finding new bacterial targets. Thus, although causality of the gut microbiota in various diseases still needs to be proven, FMT may prove to be a powerful tool providing us with diagnostic and therapeutic leads.

Osteomicrobiology: A New Cross-Disciplinary Research Field

The mutualistic interaction between the gut microbiota (GM) and its host profoundly shapes many aspects of our physiology. The composition and activity of the gut microbiota is modulated by environmental factors such as dietary habits and antibiotic treatments. In rodents, studies demonstrate that the GM is a crucial regulator of bone metabolism and that modulation of the GM composition by probiotic interventions can prevent castration-induced bone loss. Short-term colonization of germ-free mice with GM results in an activation of CD4+T cells, resulting in increased levels of pro-inflammatory cytokines in bone and thereby activation of osteoclastic bone resorption. Besides these immune-mediated effects on bone mass, the GM is involved in nutritional uptake and may, thereby, regulate overall body growth and bone sizes possibly mediated via altered IGF-I levels. We recently introduced a new term "osteomicrobiology" for the rapidly emerging research field of the role of the microbiota in bone health. This research field is aimed to bridge the gaps between bone physiology, gastroenterology, immunology, and microbiology. Future studies will determine if the GM is a novel therapeutic target for osteoporosis and if the GM composition might be used as a biomarker for fracture prediction.

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi

A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon's second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults. IMPORTANCE We sought to identify the fungi that colonize healthy GI tracts and that have a sustained influence on the diverse functions of the gut microbiome. Instead, we found that all fungi in the stool of healthy volunteers could be explained by their presence in oral and dietary sources and that our results, together with those from other analyses, support the model that there is little or no gastrointestinal colonization by fungi. This may be due to Westernization, primate evolution, fungal ecology, and/or the strong defenses of a healthy immune system. Importantly, fungal colonization of the GI tract may often be indicative of disease. As fungi can cause serious infections in immunocompromised individuals and are found at increased abundance in multiple disorders of the GI tract, understanding normal fungal colonization is essential for proper treatment and prevention of fungal pathogenesis.

Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia

BACKGROUND

Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota.

RESULTS

Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth.

CONCLUSIONS

These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.

Environment dominates over host genetics in shaping human gut microbiota

Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements. We further demonstrate that microbiome data significantly improve the prediction accuracy for many human traits, such as glucose and obesity measures, compared to models that use only host genetic and environmental data. These results suggest that microbiome alterations aimed at improving clinical outcomes may be carried out across diverse genetic backgrounds.

Skin bacterial flora as a potential risk factor predisposing to late bacterial infection after cross-linked hyaluronic acid gel augmentation

Introduction

Cross-linked hyaluronic acid (HA) gel is widely used in esthetic medicine. Late bacterial infection (LBI) is a rare, but severe complication after HA augmentation. The aim of this study was to determine whether patients who underwent the HA injection procedure and developed LBI had qualitatively different bacterial flora on the skin compared to patients who underwent the procedure without any complications.

Methods

The study group comprised 10 previously healthy women with recently diagnosed, untreated LBI after HA augmentation. The control group comprised 17 healthy women who had a similar amount of HA injected with no complications. To assess the difference between the two groups, their skin flora was cultured from nasal swabs, both before and after antibiotic treatment in the study group.

Results

A significant increase in the incidence of Staphylococcus epidermidis was detected in the control group (P=0.000) compared to the study group. The study group showed a significantly higher incidence of Staphylococcus aureus (P=0.005), Klebsiella pneumoniae (P=0.006), Klebsiella oxytoca (P=0.048), and Staphylococcus haemolyticus (P=0.048) compared to the control group.

Conclusion

The bacterial flora on the skin differed in patients with LBI from the control group. The control group’s bacterial skin flora was dominated by S. epidermidis. Patients with LBI had a bacterial skin flora dominated by potentially pathogenic bacteria.

Sieving through gut models of colonization resistance

The development of innovative high-throughput genomics and metabolomics technologies has considerably expanded our understanding of the commensal microorganisms residing within the human body, collectively termed the microbiota. In recent years, the microbiota has been reported to have important roles in multiple aspects of human health, pathology and host-pathogen interactions. One function of commensals that has attracted particular interest is their role in protection against pathogens and pathobionts, a concept known as colonization resistance. However, pathogens are also able to sense and exploit the microbiota during infection. Therefore, obtaining a holistic understanding of colonization resistance mechanisms is essential for the development of microbiome-based and microbiome-targeting therapies for humans and animals. Achieving this is dependent on utilizing physiologically relevant animal models. In this Perspective, we discuss the colonization resistance functions of the gut microbiota and sieve through the advantages and limitations of murine models commonly used to study such mechanisms within the context of enteric bacterial infection.

Early microbiota, antibiotics and health

The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance. Exposure to antibiotics, either prenatally or postnatally, is common in early life mainly due to the use of intrapartum prophylaxis or to the administration of antibiotics in C-section deliveries. However, we are still far from understanding the impact of early antibiotics and their long-term effects. Increased risk of non-communicable diseases, such as allergies or obesity, has been observed in individuals exposed to antibiotics during early infancy. Moreover, the impact of antibiotics on the establishment of the infant gut resistome, and on the role of the microbiota as a reservoir of resistance genes, should be evaluated in the context of the problems associated with the increasing number of antibiotic resistant pathogenic strains. In this article, we review and discuss the above-mentioned issues with the aim of encouraging debate on the actions needed for understanding the impact of early life antibiotics upon human microbiota and health and for developing strategies aimed at minimizing this impact.

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms

The aim of this study was to investigate the fate of nine potential indicator antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, intI1) and the diversity of bacterial communities in response to poultry manure applications to arable soil over a 90 day period. Quantitative real time PCR and Illumina high-throughput sequencing of 16S rDNA gene were used to quantify and trace ARG fate. The levels of all genes dramatically decreased over time and intI1, sul1, sul2 and tetM always had the greatest abundance and lowest dissipation rates. This indicated that more effort should be focused on the ARG elimination from manure rather than waiting for subsequent attenuation in the environment. Our sequencing results documented dramatic changes in the microbial community structure and diversity during these experiments. In poultry manure groups, Bacteroidetes and Actinobacteria were the two dominant phyla while Acidobacteria dominated the control groups. Moreover, the relative abundance of genera Corynebacterium, Pseudomonas, Ochrobactrum, Actinomadura and Bacillus, which contained potential opportunistic pathogens, changed over time suggesting that poultry manure not only strongly influenced bacterial community composition, but also selected specific bacterial communities. This study provides a glimpse of ARG fates and bacterial community diversity in soil after the application of poultry manure.

Clostridium difficile - From Colonization to Infection

Clostridium difficile is the most frequent cause of nosocomial antibiotic-associated diarrhea. The incidence of C. difficile infection (CDI) has been rising worldwide with subsequent increases in morbidity, mortality, and health care costs. Asymptomatic colonization with C. difficile is common and a high prevalence has been found in specific cohorts, e.g., hospitalized patients, adults in nursing homes and in infants. However, the risk of infection with C. difficile differs significantly between these cohorts. While CDI is a clear indication for therapy, colonization with C. difficile is not believed to be a direct precursor for CDI and therefore does not require treatment. Antibiotic therapy causes alterations of the intestinal microbial composition, enabling C. difficile colonization and consecutive toxin production leading to disruption of the colonic epithelial cells. Clinical symptoms of CDI range from mild diarrhea to potentially life-threatening conditions like pseudomembranous colitis or toxic megacolon. While antibiotics are still the treatment of choice for CDI, new therapies have emerged in recent years such as antibodies against C. difficile toxin B and fecal microbial transfer (FMT). This specific therapy for CDI underscores the role of the indigenous bacterial composition in the prevention of the disease in healthy individuals and its role in the pathogenesis after alteration by antibiotic treatment. In addition to the pathogenesis of CDI, this review focuses on the colonization of C. difficile in the human gut and factors promoting CDI.

In vitro models of the human microbiota and microbiome

Gut microbiome studies have been gaining popularity over the years, especially with the development of new technologies (e.g. metataxonomics, metagenomics, metatranscriptomics, and metabonomics) that makes it easier for researchers to characterize the composition and functionality of these complex microbial communities. The goal of these studies is to identify a microorganism, group of microbes, or microbial metabolite which correlates with a disease state (e.g. inflammatory bowel disease, colorectal cancer, and obesity). Many of these are cross-sectional studies, where fecal samples from a group of diseased individuals are compared with those from a group of healthy individuals at a single time point. However, there are a wide range of variables that can affect the gut microbiota of humans which make mechanistic studies challenging. Longitudinal studies are required for research to more reliably correlate interventions or disease status to microbiota composition and functionality. However, longitudinal studies in humans and animals are difficult, expensive, and time-consuming. This review will discuss in vitro gut fermentation models and how they can be used to perform longitudinal studies that complement in vivo microbiome studies. Gut fermentation models support the growth of stable, reproducible, and diverse microbial communities in a tightly controlled environment set to mimic the conditions microbes encounter in the gastrointestinal tract. Gut fermentation models will make it easier for researchers to perform mechanistic studies and aid in the development of novel treatments that are both targeted and maintained over time.

Doxycycline induces dysbiosis in female C57BL/6NCrl mice

OBJECTIVE

This study aims to demonstrate the effect of oral doxycycline on fecal microbiota of mice. Doxycycline is a common effector for control of gene expression using the tet-inducible system in transgenic mice. The effect of oral doxycycline on murine gut microbiota has not been reported. We evaluated the effect of doxycycline treatment by sequencing the V4 hypervariable region of the 16S rRNA gene from fecal samples collected during a 4 week course of treatment at a dose of 2 mg/ml in the drinking water.

RESULTS

The fecal microbiota of treated animals were distinct from control animals; the decreased richness and diversity were characterized primarily by Bacteroides sp. enrichment. These effects persisted when the treatment was temporarily discontinued for 1 week. These data suggest that doxycycline treatment can induce significant dysbiosis, and its effects should be considered when used in animal models that are or maybe sensitive to perturbation of the gut microbiota.

Early-Life Intestine Microbiota and Lung Health in Children

The gastrointestinal microbiota plays a critical role in nutritional, metabolic, and immune functions in infants and young children and has implications for future lung health status. Understanding the role of intestinal dysbiosis in chronic lung disease progression will provide opportunities to design early interventions to improve the course of the disease. Gut microbiota is established within the first 1 to 3 years of life and remains relatively stable throughout the life span. In this review, we report the recent development in research in gut-lung axis, with focus on the effects of targeting microbiota of infants and children at risk of or with progressive lung diseases. The basic concept is to exploit this approach in critical window to achieve the best results in the control of future health.

Microbial community response during the treatment of pharmaceutically active compounds (PhACs) in constructed wetland mesocosms

The presence of pharmaceutically active compounds (PhACs) in wastewater treatment plant effluent poses a potential risk to aquatic ecosystems. Constructed wetlands have recently been used to control PhACs. However, the microbial communities that are involved in these processes have not been comprehensively investigated. This study aimed to evaluate the removal of PhACs and microbial response in constructed wetlands during the treatment of PhACs. The effects of PhACs on bacterial communities in constructed wetland mesocosms were analyzed by Illumina MiSeq sequencing technology. Results indicated that removal efficiencies of PhACs were enhanced over time, and constructed wetlands offer higher removal efficiencies for the PhACs studied compared to conventional wastewater treatment plants. Plants improved microbial richness and diversity while both indices were negatively correlated with PhAC concentrations ranging from 30 to 500 μg/L in constructed wetland mesocosms. The microbial communities of the constructed wetland mesocosms were dominated by Proteobacteria, Acidobacteria, and Bacteroidetes under PhAC exposure, while Desulfobulbus and Treponema were the dominant genera. In particular, Proteobacteria were correlated with PhAC concentrations. Overall, this study provides valuable microbial community ecology data to understand how microbial populations respond to PhAC stress in constructed wetlands.

Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine

After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, the feeding environment, including the composition of animal intestinal microbiota, has changed rapidly. We hypothesized that the microbial genomes have also been affected by this legal prohibition, and investigated an important member of the swine gut microbiota, Lactobacillus salivarius, with a pan-genomic approach. Here, we isolated 21 L. salivarius strains composed of 6 strains isolated before the AGP prohibition (SBPs) and 15 strains isolated after the AGP prohibition (SAPs) at an interval of a decade, and the draft genomes were generated de novo. Several genomic differences between SBPs and SAPs were identified, although the number and function of antibiotic resistance genes were not different. SBPs showed larger genome size and a higher number of orthologs, as well as lower genetic diversity, than SAPs. SBPs had genes associated with the utilization of L-rhamnose and D-tagatose for energy production. Because these sugars are also used in exopolysaccharide (EPS) synthesis, we tried to identify differences in biofilm formation-associated genes. The genes for the production of EPSs and extracellular proteins were different in terms of amino acid sequences. Indeed, SAPs formed dense biofilm and survived better than SBPs in the swine intestinal environment. These results suggest that SAPs have evolved and adapted to protect themselves from new selection pressure of the swine intestinal microenvironment by forming dense biofilms, adopting a distinct antibiotic resistance strategy. This finding is particularly important to understand the evolutionary changes in host-microbe interaction and provide detailed insight for the development of effective probiotics for livestock.