Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment

Antibioottihäiriöt kokeellisessa mikrobiyhteisössä

Tässä tutkimuksessa tarkasteltiin antibiootin aiheuttamia häiriöitä bakteeripopulaatioissa. Häiriöt ovat yleisiä ekosysteemeissä ja ne voivat aiheuttaa huomattavia muutoksia yhteisökoostumukseen ja yhteisön toimintaan. Yhteisön vaste määräytyy ekologisten ja evolutiivisten tekijöiden perusteella: häiriöt muuttavat lajien kilpailukykyä yhteisössä, mutta lajien nopea evoluutio voi vaikuttaa lajien kohtaloon. Tässä tutkielmassa keskityttiin pääasiassa häiriöiden ekologisiin vaikutuksiin. Häiriön yhteisövasteen parempi ymmärtäminen on tärkeää yleisesti sekä käytännön kysymysten kannalta niin antibioottihäiriöiden osalta kuin esimerkiksi yhteisöissä, jotka ovat häiriintyneet ilmastonmuutoksen tai erilaisten kemikaalien takia. Tähän asti suurin osa tutkimuksista on käyttänyt yksi- tai kaksilajisia yhteisöjä, jolloin mahdolliset yhteisövaikutukset yhden lajin kohtaloon jäävät huomioimatta. Antibiootti häiriöitä tutkittiin altistamalla monilajinen bakteeriyhteisö kolmelle eritasoiselle streptomysiinipulssille. Yhteisökoostumuksen muutoksia tutkittiin pulssin lopussa (ekologinen vastustuskyky) ja antibioottipulssin päättymisen ja yhteisön toipumisen jälkeen (palautumiskyky) verraten häiriötä edeltäneeseen yhteisökoostumukseen. Yhteisöön saapuvaa lajivirtaa manipuloimalla tutkittiin parantaisiko se yhteisön vastustus- ja palautumiskykyä. Analyysien perusteella jopa matalilla antibioottikonsentraatioilla voi olla pitkäaikaisia vaikutuksia yhteisökoostumukseen, joskin vaikutuksen suuruusluokka riippui antibioottipitoisuudesta. Yhteisöjen monimuotoisuus palautui koostumusta paremmin etenkin heikompien häiriöiden jälkeen. Lajivirta edesauttoi yhteisöjen palautumista, mutta ei vaikuttanut niiden ekologiseen vastustuskykyyn. Tulokset olivat suhteellisen toistettavia rinnakkaisyhteisöjen välillä, ja lajien ominaisuudet ohjasivat lajien kohtaloa, mikä viittaa determinististen ekologisten prosessien ohjaavan yhteisövastetta. Kuitenkin toistettavuus väheni yhteisöissä, jotka oli altistettu korkeimman konsentraation antibioottihäiriölle, mikä puolestaan voi viitata evoluutioon.The purpose of this thesis was to study the antibiotic perturbations in bacterial populations. Perturbations are common in ecosystems and they can change the composition and functionality of a community substantially. The response of a community is governed by ecological and evolutionary factors: perturbations change the competitive ability of species in the community, but rapid evolution can further affect species fate. This thesis focuses more on the ecological effects. Understanding the community response to a disturbance would be interesting both from a general point of view and from the more practical approach of understanding natural communities under perturbations caused by antibiotics but also, for example, by climate change or chemicals. Thus far, most studies have been performed in one- or two-species systems, not taking into account the effects communities have on the fate of a single species. To study antibiotic perturbations, a multi-species bacterial community was exposed to a streptomycin pulse of three different levels concentrations. Changes in community composition were studied in the end of the pulse (ecological resistance) and after a recovery period (resilience) from the antibiotic perturbation comparing to the pre-perturbed communities. Further, the presence of species flow was manipulated to examine if it could enhance community resistance and resilience. Based on the analysis, even low antibiotic concentrations can have a long-lasting effect on community composition, but the magnitude of the effect is dependent on the concentration. Community diversity was recovered better than the composition, especially after the weaker perturbations. Species flow aids in community recovery but does not affect resistance. The results were relatively reproducible between replicate communities, and species traits steered the species fate in, pointing to deterministic ecological processes driving the community response. However, repeatability decreased in communities perturbed with the highest antibiotic concentration, which could point to evolution

Microbiota-Immune System Interactions in Diet-Induced Metabolic Syndrome

Metabolic syndrome (MetS) is the collective term for the interrelated abnormalities associated with obesity. Features of MetS promote a variety of chronic diseases that are amongst humanity’s most pressing public-health problems. MetS is increasingly appreciated to be associated with chronic inflammation driven by an imbalance of host immune cells and expression of pro-inflammatory cytokines. While numerous genetic factors influence the development of MetS, the increased incidence of this disorder occurring amidst changes in food production and dietary habits has led to the presumption that diet and the intestinal microbiota is a major determinant of MetS. The overall goal of my studies was to investigate this hypothesis. First, I sought to identify microbiota-based markers that might predict diet-induced obesity. Targeted and untargeted approaches were utilized including 16S rRNA gene amplicon sequencing for microbiome profiling and a TMT-based multiplexed mass spectrometry approach for analysis of the fecal metaproteome. Notably, we show that the fecal metaproteome appears to be a promising candidate for distinguishing differential responses to high-fat diets (HFD) and provides insight into potential mechanisms regarding the host-microbiota interactions mediating response to HFD exposure and highlights putative biomarkers for predicting obesity. Next, I explored gut-bacterial derived activators of innate-immune signaling as key drivers of adipose inflammation and insulin resistance that results from HFD. Hence, another goal of this study was to examine how ablation of gut microbiota influenced HFD-induced inflammation utilizing three approaches to alter microbiota; antibiotics, germ-free mice, and Altered Schaedler Flora mice. We described HFD–induced, microbiota-dependent changes in immune cell populations in adipose tissue that associated with pro-inflammatory gene expression and features of MetS. Lastly, I sought to ameliorate the inflammation that promotes MetS. One common feature of inflammation-associated microbiotas is increased levels of flagellin believed to cause intestinal inflammation due to flagellin’s ability to activate pro-inflammatory gene expression. Hence, I hypothesize that boosting levels of flagellin-specific IgA may help regulate flagellated bacteria and, protect against development of intestinal inflammation. Herein, we describe that administration of purified flagellin elicits a robust anti-flagellin fecal IgA response that reshapes microbiota composition, reduces flagellin expression, and protects against experimental colitis and MetS

The gut microbiome modulates post stroke outcome

15 million people suffer from stroke per year. Fundamentally, stroke is caused by a lack of oxygenated blood to brain tissue which results in tissue death. This entails a complex pathophysiology which encompasses 3 phases. Within minutes to hours, brain resident cells initiate excitotoxicity leading to irreversible neuronal death. From days to months, peripheral recruitment of immune cells to the brain drives neuroinflammation and exacerbates stroke outcome. Finally, within months to years, there is an increase in neuronal plasticity which enables reorganisation of cortical networks and restoration of broken circuits. Despite decades of research and intricate understanding of the physiological processes occurring after stroke, only one acute therapy is approved for use in clinics. An interesting therapeutic target for scientific researchers is modulation of the peripheral host immune system. Experimental research has shown that polarisation of the immune cell sub populations towards pro-/anti-inflammatory state can exacerbate or alleviate stroke outcome respectively. Polarised immune cell subsets migrate from peripheral secondary lymphoid organs to the brain lesion. While the intestinal immune compartment contains the majority of the immune cells in the body, it is the intestinal lumen that is the home to 1000 different readily adapting bacterial species. The gut microbiota has been shown to intimately interact with the immune system and alter the function of particular immune cell subsets. Recent experimental evidence has indicated a potential role for the interaction the gut microbiota and immune system in brain disease. We hypothesised that the gut microbiota could therefore play a role in the outcome of stroke. Within this thesis we explore the gut microbiota and its derived metabolites in experimental ischemic stroke models. This thesis incorporates four publications which have unravelled different aspects of how the gut microbiota affects stroke. The key experimental findings within this thesis can be summarised in five key concepts. 1) The gut microbiota and stroke have a bidirectional interaction, both having the ability to change the other. 2) The gut microbiota alters peripheral immune cells which after stroke, were shown to migrate to the brain and alter the inflammatory milieu. 3) The presence of the gut microbiota, or treatment with healthy gut microbiota transfer, improved stroke outcome. 4) Small changes in the gut microbiota can alter response to stroke immunotherapies. 5) Short-chain fatty acids, the dietary metabolites derived from the gut microbiota, improve functional post stroke recovery. Taken together, I hope this thesis reflects and demonstrates the interesting therapeutic potential of gut microbiota manipulation for treatment of stroke. The addition of microbiota-based treatments may not only be a stand-alone therapy to aid recovery after stroke, but additionally could be a practical add-on for existing procedural treatments

Modelling the effects of microbial transmission and human culture on host-mutualist association

Humans harbour diverse microbial communities, and this interaction has fitness consequences for hosts and symbionts. Understanding the mechanisms that preserve host-symbiont association is an important step in studying co-evolution between humans and their mutualist microbial partners. This association is promoted by faithful vertical transmission; however, vertical transmission is known to be imperfect. Therefore, it is crucial to understand how birth and feeding modes affect the establishment of microbiota. In general, cultural practices of the host are expected to be important in microbial transmission as they influence the host's interaction with the environment. There is a need to understand whether and how cultural practices affect host-microbe associations. The human gut microbiota is transmitted from mother to infant through vaginal birth and breastfeeding. In this thesis, chapter 2 develops a mathematical model to show how early life events affect competition between mutualists and commensals and microbe-host-immune interactions to cause long-term alterations in gut microbial profiles. This model shows that microbe-microbe and microbe-host interactions shape the gut populations following different birth and feeding modes. It is unclear whether host-microbe associations can generally be maintained despite imperfect vertical transmission over many generations. Chapter 3 develops a mathematical model to identify the conditions under which a mutualist can persist in a population when vertical transmission is imperfect. To study the evolution of mutualists over time, chapter 4 introduces another type of mutualist to the population, and investigates the conditions that allow this new species to establish. The models show that several factors compensate for imperfect vertical transmission, namely, a selective advantage to the host conferred by the mutualist, horizontal transmission of the mutualist through an environmental reservoir, and cultural transmission of a practice that promotes microbial transmission. These factors strengthen the host-microbe association, and encourage the establishment of a new species allowing some degree of microbial competition. My models highlight the importance of microbe-microbe interaction in shaping the evolution of gut species. A cooperative microbial relationship promotes the co-existence of a pre-established mutualist and a new species even when this species is harmful to the host (pathogenic)

Emerging Priorities for Microbiome Research

Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19–23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab’s findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration

Modelling microbiome recovery after antibiotics using a stability landscape framework

Treatment with antibiotics is one of the most extreme perturbations to the human microbiome. Even standard courses of antibiotics dramatically reduce the microbiome’s diversity and can cause transitions to dysbiotic states. Conceptually, this is often described as a ‘stability landscape’: the microbiome sits in a landscape with multiple stable equilibria, and sufficiently strong perturbations can shift the microbiome from its normal equilibrium to another state. However, this picture is only qualitative and has not been incorporated in previous mathematical models of the effects of antibiotics. Here, we outline a simple quantitative model based on the stability landscape concept and demonstrate its success on real data. Our analytical impulse-response model has minimal assumptions with three parameters. We fit this model in a Bayesian framework to data from a previous study of the year-long effects of short courses of four common antibiotics on the gut and oral microbiomes, allowing us to compare parameters between antibiotics and microbiomes, and further validate our model using data from another study looking at the impact of a combination of last-resort antibiotics on the gut microbiome. Using Bayesian model selection we find support for a long-term transition to an alternative microbiome state after courses of certain antibiotics in both the gut and oral microbiomes. Quantitative stability landscape frameworks are an exciting avenue for future microbiome modelling

Microbiota regulate short chain fatty acids and influence histone acylations in intestinal epithelial cells.

The intestinal microbiota have a vital role in aiding digestion by metabolising dietary fibres. In this process, they produce short chain fatty acids (SCFAs) such as butyrate, an important energy source for intestinal epithelial cells. SCFAs are chemically related to histone acylations, a growing number of post-translational modifications that include histone acetylation, butyrylation and crotonylation. Histone post-translational modifications are thought to be involved in the regulation of gene expression as they can specifically recruit transcription factors and chromatin remodellers. Histone acylations are abundant in the intestine and are associated with active chromatin. In this project, I have identified that butyrate can upregulate histone acylations in both colon carcinoma cells and intestinal organoids in a dynamic manner. In addition, I identified that class I histone deacetylases (HDACs) are efficient histone decrotonylases. I have achieved this through a combination of biological analysis of the effects of treatment with HDAC inhibitors and in vitro analysis of purified proteins, which enabled determination of kinetic parameters. When investigating how SCFAs could influence histone acylations in vivo, I identified that antibiotic induced depletion of the microbiota in mice caused reduction in luminal SCFA concentration and global changes in histone acetylation and crotonylation, particularly those at histone H4. RNA-sequencing of these mice identified changes in the expression of genes which were involved in many important biological processes, such as cell signalling, energy generation and metabolism. Further to this, I studied lysine crotonylation and H4K8 acetylation at dysregulated genes to understand the how the presence of these modifications at the promoter influences gene expression in this context. These intriguing findings suggest that histone acylations could act as a nutrient sensors to couple changes in microbiota composition to that of gene expression and cellular function