Commensal Population Research Articles

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.

Bacterial chondronecrosis with osteomyelitis related Enterococcus cecorum isolates are genetically distinct from the commensal population and are more virulent in an embryo mortality model

Bacterial chondronecrosis with osteomyelitis (BCO) is a common cause of broiler lameness. Bacteria that are found in BCO lesions are intestinal bacteria that are proposed to have translocated through the intestinal epithelium and have spread systemically. One of the specific bacterial species frequently isolated in BCO cases is Enterococcus cecorum. In the current study, caecal isolates were obtained from birds derived from healthy flocks (12 isolates from 6 flocks), while isolates derived from caeca, colon, pericardium, caudal thoracic vertebrae, coxo-femoral joint, knee joint and intertarsal joint (hock) were obtained from broilers derived from BCO outbreaks (111 isolates from 10 flocks). Pulsed field gel electrophoresis was performed to determine similarity. Clonal E. cecorum populations were isolated from different bones/joints and pericardium from animals within the same flock, with intestinal strains carrying the same pulsotype, pointing to the intestinal origin of the systemically present bacteria. Isolates from the intestinal tract of birds from healthy flocks clustered away from the BCO strains. Isolates from the gut, bones/joints and pericardium of affected animals contained a set of genes that were absent in isolates from the gut of healthy animals, such as genes encoding for enterococcal polysaccharide antigens (epa genes), cell wall structural components and nutrient transporters. Isolates derived from the affected birds induced a significant higher mortality in the embryo mortality model as compared to the isolates from the gut of healthy birds, pointing to an increased virulence.

Fecal microbiota transplantation and short-chain fatty acids reduce sepsis mortality by remodeling antibiotic-induced gut microbiota disturbances.

Sepsis is the leading cause of death in critically ill patients. The gastrointestinal tract has long been thought to play an important role in the pathophysiology of sepsis. Antibiotic therapy can reduce a patient's commensal bacterial population and raise their risk of developing subsequent illnesses, where gut microbiota dysbiosis may be a key factor. In this study, we analyzed the 16S rRNA of fecal samples from both healthy people and patients with sepsis to determine if alterations in gut bacteria are associated with sepsis. Then, we developed a mouse model of sepsis using cecal ligation and puncture (CLP) in order to examine the effects of fecal microbiota transplantation (FMT) and short-chain fatty acids (SCFAs) on survival rate, systemic inflammatory response, gut microbiota, and mucosal barrier function. Sepsis patients' gut microbiota composition significantly differed from that of healthy people. At the phylum level, the amount of Proteobacteria in the intestinal flora of sepsis patients was much larger than that of the control group, whereas the number of Firmicutes was significantly lower. Mice with gut microbiota disorders (ANC group) were found to have an elevated risk of death, inflammation, and organ failure as compared to CLP mice. However, all of these could be reversed by FMT and SCFAs. FMT and SCFAs could regulate the abundance of bacteria such as Firmicutes, Proteobacteria, Escherichia Shigella, and Lactobacillus, restoring them to levels comparable to those of healthy mice. In addition, they increased the expression of the Occludin protein in the colon of mice with sepsis, downregulated the expression of the NLRP3 and GSDMD-N proteins, and reduced the release of the inflammatory factors IL-1β and IL-18 to inhibit cell pyroptosis, ultimately playing a protective role in sepsis. FMT and SCFAs provide a microbe-related survival benefit in a mouse model of sepsis, suggesting that they may be a viable treatment for sepsis.

Comparative study on bacterial flora of oral cavity of smokers and non-smokers

The oral cavity is a complex heterogeneous microbial habitat. The presence of nutrients, saliva and epithelial debris make the mouth favorable habitat for great variety of bacteria. Cigarette smoking is a public health problem. It decreases the commensal population of oral cavity resulting in an increase of pathogenic microbes. The study was designed to compare the bacterial flora of oral cavity of smokers and non-smokers and their antibiotic sensitivity pattern. Twelve individuals comprising of 6 smokers and 6 nonsmokers were enrolled for the study. Oral swabs were collected from the oral cavity using sterile cotton swab stick under standard aseptic methods. The specimens were subjected to microscopy and culture. Organisms were identified using standard microbiological techniques. Only Gram positive bacteria were isolated from oral cavity of both smokers and non-smokers. Higher rates of bacteria were isolated from oral cavity of non-smokers (55%) than smokers (45%). Streptococcus species were found to be prevalent in both smokers and non-smokers. Streptococcus mutans (28.57%) and Streptococcus salivarius (28.57%) was found to be the most dominant bacteria in smokers. While Staphylococcus epidermidis (33.33%) was found to be most prevalent bacteria among non-smokers. Our study suggests that smoking may have altered bacterial acquisition. The study also showed the prevalence of potential pathogens and lesser number of commensals in oral cavity of smokers. The presence of potential pathogens may lead to greater susceptibility to oral as well as respiratory infections. Antibiotic susceptibility test showed higher resistivity of bacteria isolated from oral cavity of smokers towards commonly used antibiotics in comparison to non-smokers. This study suggests that campaign against smoking should be intensified and more people should be aware about the effect of smoking on oral microbiome and related diseases.

Biofilms and Benign Colonic Diseases.

The colon has a very large surface area that is covered by a dense mucus layer. The biomass in the colon includes 500-1000 bacterial species at concentrations of ~1012 colony-forming units per gram of feces. The intestinal epithelial cells and the commensal bacteria in the colon have a symbiotic relationship that results in nutritional support for the epithelial cells by the bacteria and maintenance of the optimal commensal bacterial population by colonic host defenses. Bacteria can form biofilms in the colon, but the exact frequency is uncertain because routine methods to undertake colonoscopy (i.e., bowel preparation) may dislodge these biofilms. Bacteria in biofilms represent a complex community that includes living and dead bacteria and an extracellular matrix composed of polysaccharides, proteins, DNA, and exogenous debris in the colon. The formation of biofilms occurs in benign colonic diseases, such as inflammatory bowel disease and irritable bowel syndrome. The development of a biofilm might serve as a marker for ongoing colonic inflammation. Alternatively, the development of biofilms could contribute to the pathogenesis of these disorders by providing sanctuaries for pathogenic bacteria and reducing the commensal bacterial population. Therapeutic approaches to patients with benign colonic diseases could include the elimination of biofilms and restoration of normal commensal bacteria populations. However, these studies will be extremely difficult unless investigators can develop noninvasive methods for measuring and identifying biofilms. These methods that might include the measurement of quorum sensing molecules, measurement of bile acids, and identification of bacteria uniquely associated with biofilms in the colon.

Global Stability of Symbiotic Model of Commensalism and Parasitism with Harvesting in Commensal Populations

This article revisit the stability property of symbiotic model of commensalism and parasitism with harvesting in the commensal population. The model was proposed by Nurmaini Puspitasari, Wuryansari Muharini Kusumawinahyu, Trisilowati (Dynamic analysis of the symbiotic model of commensalism and parasitism with harvesting in commensal populations, Jurnal Teori dan Aplikasi Matematika, 2021, 5(1): 193-204). By establishing three powerful Lemmas, sufficient conditions which ensure the global stability of the equilibria are obtained.

Stability property of the boundary equilibria of a symbiotic model of commensalism and parasitism with harvesting in commensal populations

<abstract><p>This article demonstrates the stability property of two boundary equilibria of a symbiotic model of commensalism and parasitism with harvesting in the commensal population. The model was proposed by Nurmaini Puspitasari, Wuryansari Muharini Kusumawinahyu, Trisilowati (2021). We first give two numeric examples to show that the corresponding results of the mentioned paper may be incorrect. Then, by analysis of the characteristic roots of the characteristic equations, we obtain sufficient conditions that ensure the locally asymptotic stability of the equilibria. After that, by applying the standard comparison theorem, some novel results on the global attractivity of these two equilibria are obtained respectively. Our results complement and supplement some known results.</p></abstract>

Dynamical Analysis of the Symbiotic Model of Commensalism in Four Populations with Michaelis-Menten type Harvesting in the First Commensal Population

Dynamical Analysis of the Symbiotic Model of Commensalism in Four Populations with Michaelis-Menten type Harvesting in the First Commensal Population

The Gut-Brain Axis in Multiple Sclerosis. Is Its Dysfunction a Pathological Trigger or a Consequence of the Disease?

A large and expending body of evidence indicates that the gut-brain axis likely plays a crucial role in neurological diseases, including multiple sclerosis (MS). As a whole, the gut-brain axis can be considered as a bi-directional multi-crosstalk pathway that governs the interaction between the gut microbiota and the organism. Perturbation in the commensal microbial population, referred to as dysbiosis, is frequently associated with an increased intestinal permeability, or “leaky gut”, which allows the entrance of exogeneous molecules, in particular bacterial products and metabolites, that can disrupt tissue homeostasis and induce inflammation, promoting both local and systemic immune responses. An altered gut microbiota could therefore have significant repercussions not only on immune responses in the gut but also in distal effector immune sites such as the CNS. Indeed, the dysregulation of this bi-directional communication as a consequence of dysbiosis has been implicated as playing a possible role in the pathogenesis of neurological diseases. In multiple sclerosis (MS), the gut-brain axis is increasingly being considered as playing a crucial role in its pathogenesis, with a major focus on specific gut microbiota alterations associated with the disease. In both MS and its purported murine model, experimental autoimmune encephalomyelitis (EAE), gastrointestinal symptoms and/or an altered gut microbiota have been reported together with increased intestinal permeability. In both EAE and MS, specific components of the microbiota have been shown to modulate both effector and regulatory T-cell responses and therefore disease progression, and EAE experiments with germ-free and specific pathogen-free mice transferred with microbiota associated or not with disease have clearly demonstrated the possible role of the microbiota in disease pathogenesis and/or progression. Here, we review the evidence that can point to two possible consequences of the gut-brain axis dysfunction in MS and EAE: 1. A pro-inflammatory intestinal environment and “leaky” gut induced by dysbiosis could lead to an altered communication with the CNS through the cholinergic afferent fibers, thereby contributing to CNS inflammation and disease pathogenesis; and 2. Neuroinflammation affecting efferent cholinergic transmission could result in intestinal inflammation as disease progresses.

Dynamic Analysis of the Symbiotic Model of Commensalism and Parasitism with Harvesting in Commensal Populations

This article discussed about a dynamic analysis of the symbiotic model of commensalism and parasitism with harvesting in the commensal population. This model is obtained from a modification of the symbiosis commensalism model. This modification is by adding a new population, namely the parasite population. Furthermore, it will be investigated that the three populations can coexist. The analysis carried out includes the determination of all equilibrium points along with their existence and local stability along with their stability requirements. From this model, it is obtained eight equilibrium points, namely three population extinction points, two population extinction points, one population extinction point and three extinction points can coexist. Of the eight points, only two points are asymptotically stable if they meet certain conditions. Next, a numerical simulation will be performed to illustrate the model’s behavior. In this article, a numerical simulation was carried out using the RK-4 method. The simulation results obtained support the results of the dynamic analysis that has been done previously.This article discussed about a dynamic analysis of the symbiotic model of The dynamics of the symbiotic model of commensalism and parasitism with harvesting in the commensal population. is the main focus of this study. This model is obtained from a modification of the symbiosis commensalism model. This modification is by adding a new population, namely the parasite population. Furthermore, it will be investigated that the three populations can coexist. The analysis carried out includes the determination begins by identifying the conditions for the existence of all equilibrium points along with their existence and local stability along with their stability requirements. From this model, it is obtained eight equilibrium points, namely three population extinction points, two population extinction points, one population extinction point and three extinction points can coexist. Of the eight points, only two points are asymptotically stable if they meet certain conditions. Next, a numerical simulation will be performed to illustrate the model’s behavior. In this article, a numerical simulation was carried out using the RK-4 method. The simulation results obtained support the results of the dynamic analysis that has been done previously.[VM1] [VM1]To add a mathematical effect to the article. There can be added mathematical models produced in the study at the end of this section.

Population Density and Temperature Influence the Return on Maternal Investment in Wild House Mice

In mammals, reproduction is influenced by sexual competition, temperature and food availability and these factors might be crucial already during early life. Favorable early life environment and high maternal investment are expected to improve survival and reproduction. For example, in mammals, maternal investment via lactation predicts offspring growth. As body mass is often associated with fitness consequences, females have the potential to influence offspring fitness through their level of investment, which might interact with effects of population density and temperature. Here, we investigate the relationship between house mouse (Mus musculus domesticus) pup body mass at day 13 (used as approximation for weaning mass) and individual reproductive parameters, as well as longevity, under natural variation in population density and temperature (as approximation for season). Further, we assessed the extent to which mothers influence the body mass of their offspring until weaning. To do so, we analyzed life data of 384 house mice from a free-living wild commensal population that was not food limited. The mother’s contribution accounted for 49% of the variance in pup body mass. Further, we found a complex effect of population density, temperature and maternal investment on life-history traits related to fitness: shorter longevity with increasing pup body mass at day 13, delayed first reproduction of heavier pups when raised at warmer temperatures, and increased lifetime reproductive success for heavier pups at high densities. Our study shows that the effects of maternal investment are not independent of the effects of the environment. It thus highlights the importance of considering ecological conditions in combination with maternal effects to unravel the complexity of pup body mass on fitness measures.

Fungal infections in transplant recipients: pros and cons of immunosuppressive and antimicrobial treatment

Fungal infections in transplant recipients: pros and cons of immunosuppressive and antimicrobial treatment

Serosurvey and molecular detection of the main zoonotic parasites carried by commensal Rattus norvegicus population in Tehran, Iran

BackgroundRattus norvegicus are reservoirs for transmission of various zoonotic parasites, and they have become a threat to public health worldwide. Given the large number and the significant presence of R. norvegicus throughout the city of Tehran, this study aims to assess the frequency of zoonotic parasites carried by commensal rodents wandering in Tehran, Iran. The study considered the north, south, west, east, and center regions of Tehran for the purposes of this study. The serological tests were applied in order to detect effective antibodies against Trichomonas vaginalis (T. vaginalis), Babesia spp., and Cryptosporidium spp. using a commercial qualitative rat ELISA kit. The frequency of Toxoplasma gondii (T. gondii) was surveyed by using the conventional PCR method. Furthermore, nested PCR was employed to detect the presence of Giardia spp. and Leishmania spp. in commensal R. norvegicus dispersed in Tehran.ResultsApproximately, 76% of the 100 R. norvegicus tested were infected with at least one zoonotic parasite, indicating the significant frequency of parasites within the study areas. Seroreactivity against T. vaginalis, Babesia spp., and Cryptosporidium spp. was detected in 5%, 0%, and 1% of the R. norvegicus tested, respectively. T. gondii DNA was detected in 32 out of 100 (32%) R. norvegicus. In addition, Leishmania spp. and Giardia spp. DNA were found in 18 out of 100 (18%) and 76 out of 100 (76%) R. norvegicus investigated, respectively. T. vaginalis with 15% and T. gondii with 70% had the highest frequency of parasites among the R. norvegicus collected from the western and northeastern regions of Tehran, respectively. Moreover, Giardia spp. with 95% and Leishmania spp. with 30% had the highest frequency in the east and center districts, respectively.ConclusionThe findings showed a wide geographical dissemination of Giardia spp., Toxoplasma gondii, and Leishmania spp. in R. norvegicus within five districts of Tehran. In contrast, other parasites such as Cryptosporidium spp. infection were rarely detected in Rattus populations. No evidence for the circulation of Babesia spp. was found in this study.

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects.

Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.

Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan.

There is accumulating evidence in the biomedical literature suggesting the role of smoking in increasing the risk of oral diseases including some oral cancers. Smoking alters microbial attributes of the oral cavity by decreasing the commensal microbial population and increasing the pathogenic microbes. This study aims to investigate the shift in the salivary microbiota between smokers and non-smokers in Jordan. Our methods relied on high-throughput next-generation sequencing (NGS) experiments for V3-V4 hypervariable regions of the 16S rRNA gene, followed by comprehensive bioinformatics analysis including advanced multidimensional data visualization methods and statistical analysis approaches. Six genera—Streptococcus, Prevotella, Vellionella, Rothia, Neisseria, and Haemophilus—predominated the salivary microbiota of all samples with different percentages suggesting the possibility for the salivary microbiome to restored after quitting smoking. Three genera—Streptococcus, Prevotella, and Veillonella—showed significantly elevated levels among smokers at the expense of Neisseria in non-smokers. In conclusion, smoking has a definite impact on shifting the salivary microbiota in smokers. We can suggest that there is microbial signature at the genera level that can be used to classify smokers and non-smokers by Linear Discriminant Analysis Effect Size (LEfSe) based on the salivary abundance of genera. Proteomics and metabolomics studies are highly recommended to fully understand the effect of bacterial endotoxin release and xenobiotic metabolism on the bacterial interrelationships in the salivary microbiome and how they affect the growth of each other in the saliva of smokers.

Gut eosinophils and their impact on the mucus‐resident microbiota

SummaryThe gut has the largest commensal bacterial population in the body and its composition can be impacted by host factors such as production of immunoglobulin A (IgA). Eosinophils in the gut have been implicated in the production of antibacterial factors and maintenance of IgA‐secreting plasma cells. We used an eosinophil‐deficient mouse (∆dblGATA‐1 −/−) and littermate controls to investigate the role of eosinophils in the regulation of the microbiota, with particular emphasis on mucus‐resident species in the small and large intestine. We found no differences in IgA production or IgA‐expressing plasma cells between naive littermates in the small or large intestine. However, denaturing gel gradient electrophoresis revealed differences in the bacterial communities of the mucus and stools between wild‐type mice and ∆dblGATA‐1 −/− mice, with the greatest separation between the mucus microbial communities. Mucus‐resident bacteria in ∆dblGATA‐1 −/− mice had reduced diversity in the mucus compared with the stools. A quantitative PCR panel of selected bacteria showed that the most significant differences in the microbiota were between mucus‐resident bacteria and those in stool, such as the abundance of Clostridiales and Bacteroides. Our data implicate eosinophils in the regulation of the microbiota, especially the bacteria most hyperlocal to the gut barrier. Although we see differences between host genotypes in the overall microbial communities, further work is required to establish specifically which bacteria are different between these groups. Most importantly, the data revealed that the mucus and stool microbiota are discrete communities. Stool analysis alone may be insufficient to comprehensively explore and define the role of the gut microbiota in health and disease.

Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants.

Commensal bacterial population is believed to be a reservoir for antibiotic resistance genes (ARGs). The infant gut microbiota has relatively higher abundance of ARGs than the adults. These genes can get transferred from commensals to pathogens by horizontal gene transfer, which magnifies the spectrum of antibiotic resistance in the environment. The presence of ARGs in neo-nates and infants, with no prior antibiotic exposure, questions their origin in the naïve commensal population. Breast milk microbiota that is responsible for the initial seeding of infant gut microbiota has also been found to harbour a vast array of ARGs. This review discusses the recent findings that indicate the potential of breast milk microbiota to act as a vehicle for transmission of ARGs to infants.

Impact of Pristine Graphene on Intestinal Microbiota Assessed Using a Bioreactor-Rotary Cell Culture System.

The increased use of graphene in consumer products such as food contact materials requires a thorough understanding of its effects on the gastrointestinal commensal bacterial population. During the first phase of study, three representative commensal bacterial species (L. acidophilus, B. longum, and E. coli) were exposed to different concentrations (1, 10, and 100 μg/mL) of pristine graphene for 3, 6, and 24 h in the Bioreactor Rotary Cell Culture System (BRCCS) which allowed a continuous interaction of intestinal microbiota with the pristine graphene without precipitation of test material. The results showed that pristine graphene had dose-dependent effects on the growth of selective bacteria. To study the interaction of graphene with more diverse consortia of intestinal microbiota, fresh fecal samples from laboratory rats were used. Rat fecal slurry (3%) was maintained in an anaerobic environment and treated with different concentrations (1, 10, and 100 μg/mL) of pristine graphene for 3, 6, and 24 h. Counts of viable aerobic and anaerobic bacteria were assessed and fecal slurries were also collected for microbial population shift analysis using quantitative real-time PCR, as well as 16s rRNA sequencing. The results showed a significant two-fold increase in both aerobic and anaerobic bacterial counts (expressed as colony forming unit; CFU) during the first 3 h of exposure to all pristine graphene concentrations. However, 24 h of continuous exposure resulted in a 120% decrease in the CFU of aerobic bacteria at the highest concentration and the anaerobic bacteria CFU remained unchanged. Multivariate analysis of the q-PCR data showed that the exposure time, as well as the graphene concentrations, impacted the bacterial population abundance. Community analysis of graphene-treated fecal samples by 16S sequencing revealed significant alteration of 15 taxonomic groups, including 9 species. The increased abundance of butyrate-producing bacteria (Clostridium fimetarium, Clostridium hylemona, and Sutterella wadsworthensis) was correlated with an increase of the short-chain fatty acid, butyric acid after exposure to graphene. These results clearly indicate that graphene may cause adverse effects on the intestinal microbiome at the doses equal to 100 μg/mL. Further experiments using ex vivo intestinal explants (nonanimal model) could reveal the mechanisms by which graphene could perturb the microbe-host intestinal mucosa homeostasis.

The evolution of antibiotic resistance in a structured host population.

The evolution of antibiotic resistance in opportunistic pathogens such as Streptococcus pneumoniae, Escherichia coli or Staphylococcus aureus is a major public health problem, as infection with resistant strains leads to prolonged hospital stay and increased risk of death. Here, we develop a new model of the evolution of antibiotic resistance in a commensal bacterial population adapting to a heterogeneous host population composed of untreated and treated hosts, and structured in different host classes with different antibiotic use. Examples of host classes include age groups and geographic locations. Explicitly modelling the antibiotic treatment reveals that the emergence of a resistant strain is favoured by more frequent but shorter antibiotic courses, and by higher transmission rates. In addition, in a structured host population, localized transmission in host classes promotes both local adaptation of the bacterial population and the global maintenance of coexistence between sensitive and resistant strains. When transmission rates are heterogeneous across host classes, resistant strains evolve more readily in core groups of transmission. These findings have implications for the better management of antibiotic resistance: reducing the rate at which individuals receive antibiotics is more effective to reduce resistance than reducing the duration of treatment. Reducing the rate of treatment in a targeted class of the host population allows greater reduction in resistance, but determining which class to target is difficult in practice.

Targeting friend and foe: Emerging therapeutics in the age of gut microbiome and disease.

Mucosal surfaces that line our gastrointestinal tract are continuously exposed to trillions of bacteria that form a symbiotic relationship and impact host health and disease. It is only beginning to be understood that the cross-talk between the host and microbiome involve dynamic changes in commensal bacterial population, secretion, and absorption of metabolites between the host and microbiome. As emerging evidence implicates dysbiosis of gut microbiota in the pathology and progression of various diseases such as inflammatory bowel disease, obesity, and allergy, conventional treatments that either overlook the microbiome in the mechanism of action, or eliminate vast populations of microbes via wide-spectrum antibiotics need to be reconsidered. It is also becoming clear the microbiome can influence the body's response to therapeutic treatments for cancers. As such, targeting the microbiome as treatment has garnered much recent attention and excitement from numerous research labs and biotechnology companies. Treatments range from fecal microbial transplantation to precision-guided molecular approaches. Here, we survey recent progress in the development of innovative therapeutics that target the microbiome to treat disease, and highlight key findings in the interplay between host microbes and therapy.