Evolutionary and ecological forces that shape the bacterial communities of the human gut

Draft genome sequence of the emerging fish pathogen Flavobacterium tructae strain S12

The draft genome of Flavobacterium tructae strain S12, isolated from hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings, consisted of 5,695,942 bp, a G + C content of 35.6%, 4,775 predicted open reading frames, a putative type IX secretion system, collagenase, and hemolysin. F. tructae strains can be used as models for emerging Flavobacterium pathogens.

Fermentation technology as a driver of human brain expansion

Brain tissue is metabolically expensive. Consequently, the evolution of humans' large brains must have occurred via concomitant shifts in energy expenditure and intake. Proposed mechanisms include dietary shifts such as cooking. Importantly, though, any new food source must have been exploitable by hominids with brains a third the size of modern humans'. Here, we propose the initial metabolic trigger of hominid brain expansion was the consumption of externally fermented foods. We define "external fermentation" as occurring outside the body, as opposed to the internal fermentation in the gut. External fermentation could increase the bioavailability of macro- and micronutrients while reducing digestive energy expenditure and is supported by the relative reduction of the human colon. We discuss the explanatory power of our hypothesis and survey external fermentation practices across human cultures to demonstrate its viability across a range of environments and food sources. We close with suggestions for empirical tests.

CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance

The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.

Metabolic independence drives gut microbial colonization and resilience in health and disease

BACKGROUND

Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.

RESULTS

Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.

CONCLUSIONS

These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.

Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait

The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.

Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor

Lipopolysaccharide (LPS) is associated with chronic intestinal inflammation and promotes intestinal cancer progression in the gut. While the interplay between LPS and intestinal immune cells has been well-characterized, little is known about LPS and the intestinal epithelium interactions. In this study, we explored the differential effects of LPS on proliferation and the transcriptome in 3D enteroids/colonoids obtained from dogs with naturally occurring gastrointestinal (GI) diseases including inflammatory bowel disease (IBD) and intestinal mast cell tumor. The study objective was to analyze the LPS-induced modulation of signaling pathways involving the intestinal epithelia and contributing to colorectal cancer development in the context of an inflammatory (IBD) or a tumor microenvironment. While LPS incubation resulted in a pro-cancer gene expression pattern and stimulated proliferation of IBD enteroids and colonoids, downregulation of several cancer-associated genes such as Gpatch4, SLC7A1, ATP13A2, and TEX45 was also observed in tumor enteroids. Genes participating in porphyrin metabolism (CP), nucleocytoplasmic transport (EEF1A1), arachidonic acid, and glutathione metabolism (GPX1) exhibited a similar pattern of altered expression between IBD enteroids and IBD colonoids following LPS stimulation. In contrast, genes involved in anion transport, transcription and translation, apoptotic processes, and regulation of adaptive immune responses showed the opposite expression patterns between IBD enteroids and colonoids following LPS treatment. In brief, the crosstalk between LPS/TLR4 signal transduction pathway and several metabolic pathways such as primary bile acid biosynthesis and secretion, peroxisome, renin-angiotensin system, glutathione metabolism, and arachidonic acid pathways may be important in driving chronic intestinal inflammation and intestinal carcinogenesis.

Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma

Esophageal adenocarcinoma (EAC) claims the lives of half of patients within the first year of diagnosis, and its incidence has rapidly increased since the 1970s despite extensive research into etiological factors. The changes in the microbiome within the distal esophagus in modern populations may help explain the growth in cases that other common EAC risk factors together cannot fully explain. The precursor to EAC is Barrett's esophagus (BE), a metaplasia adapted to a reflux-mediated microenvironment that can be challenging to diagnose in patients who do not undergo endoscopic screening. Non-invasive procedures to detect microbial communities in saliva, oral swabs and brushings from the distal esophagus allow us to characterize taxonomic differences in bacterial population abundances within patients with BE versus controls, and may provide an alternative means of BE detection. Unique microbial communities have been identified across healthy esophagus, BE, and various stages of progression to EAC, but studies determining dynamic changes in these communities, including migration from proximal stomach and oral cavity niches, and their potential causal role in cancer formation are lacking. Helicobacter pylori is negatively associated with EAC, and the absence of this species has been implicated in the evolution of chromosomal instability, a main driver of EAC, but joint analyses of microbiome and host genomes are needed. Acknowledging technical challenges, future studies on the prediction of microbial dynamics and evolution within BE and the progression to EAC will require larger esophageal microbiome datasets, improved bioinformatics pipelines, and specialized mathematical models for analysis.

Running after your host: Stimulation of bacterial motility promotes colonization

In this issue of Cell Host and Microbe, Robinson et al. (2021) make elegant use of experimental evolution to demonstrate that increased motility promotes migration toward and colonization of zebrafish larvae by a commensal bacterium. Stimulation of motility depends on bacterial second messenger and on signals released by resident host microbiota.

Microbial driven genetic variation in holobionts

Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.

Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design

The importance of the gut microbiota in human health and disease progression makes it a target for research in both the biomedical and nutritional fields. To date, a number of in vitro systems have been designed to recapitulate the gut microbiota of the colon ranging in complexity from the application of a single vessel to cultivate the community in its entirety, to multi-stage systems that mimic the distinct regional microbial communities that reside longitudinally through the colon. While these disparate types of in vitro designs have been employed previously, information regarding similarities and differences between the communities that develop within was less defined. Here, a comparative analysis of the population dynamics and functional production of short-chain fatty acids (SCFAs) was performed using the gut microbiota of the same donor cultured using a single vessel and a 3-stage colon system. The results found that the single vessel communities maintained alpha diversity at a level comparable to the distal regions of the 3-stage colon system. Yet, there was a marked difference in the type and abundance of taxa, particularly between families Enterobacteriaceae, Bacteroidaceae, Synergistaceae, and Fusobacteriaceae. Functionally, the single vessel community produced significantly less SCFAs compared to the 3-stage colon system. These results provide valuable information on how culturing technique effects gut microbial composition and function, which may impact studies relying on the application of an in vitro strategy. This data can be used to justify experimental strategy and provides insight on the application of a simplified versus complex study design. KEY POINTS : • A mature gut microbiota community can be developed in vitro using different methods. • Beta diversity metrics are affected by the in vitro culturing method applied. • The type and amount of short-chain fatty acids differed between culturing methods.

Human Gut Commensal Membrane Vesicles Modulate Inflammation by Generating M2-like Macrophages and Myeloid-Derived Suppressor Cells

Immunomodulatory commensal bacteria modify host immunity through delivery of regulatory microbial-derived products to host cells. Extracellular membrane vesicles (MVs) secreted from symbiont commensals represent one such transport mechanism. How MVs exert their anti-inflammatory effects or whether their tolerance-inducing potential can be used for therapeutic purposes remains poorly defined. In this study, we show that MVs isolated from the human lactic acid commensal bacteria Pediococcus pentosaceus suppressed Ag-specific humoral and cellular responses. MV treatment of bone marrow-derived macrophages and bone marrow progenitors promoted M2-like macrophage polarization and myeloid-derived suppressor cell differentiation, respectively, most likely in a TLR2-dependent manner. Consistent with their immunomodulatory activity, MV-differentiated cells upregulated expression of IL-10, arginase-1, and PD-L1 and suppressed the proliferation of activated T cells. MVs' anti-inflammatory effects were further tested in acute inflammation models in mice. In carbon tetrachloride-induced fibrosis and zymosan-induced peritonitis models, MVs ameliorated inflammation. In the dextran sodium sulfate-induced acute colitis model, systemic treatment with MVs prevented colon shortening and loss of crypt architecture. In an excisional wound healing model, i.p. MV administration accelerated wound closure through recruitment of PD-L1-expressing myeloid cells to the wound site. Collectively, these results indicate that P. pentosaceus-derived MVs hold promise as therapeutic agents in management/treatment of inflammatory conditions.

Whole Blueberry and Isolated Polyphenol-Rich Fractions Modulate Specific Gut Microbes in an In Vitro Colon Model and in a Pilot Study in Human Consumers

Blueberry (BB) consumption is linked to improved health. The bioconversion of the polyphenolic content of BB by fermentative bacteria in the large intestine may be a necessary step for the health benefits attributed to BB consumption. The identification of specific gut microbiota taxa that respond to BB consumption and that mediate the bioconversion of consumed polyphenolic compounds into bioactive forms is required to improve our understanding of how polyphenols impact human health. We tested the ability of polyphenol-rich fractions purified from whole BB-namely, anthocyanins/flavonol glycosides (ANTH/FLAV), proanthocyanidins (PACs), the sugar/acid fraction (S/A), and total polyphenols (TPP)-to modulate the fecal microbiota composition of healthy adults in an in vitro colon system. In a parallel pilot study, we tested the effect of consuming 38 g of freeze-dried BB powder per day for 6 weeks on the fecal microbiota of 17 women in two age groups (i.e., young and older). The BB ingredients had a distinct effect on the fecal microbiota composition in the artificial colon model. The ANTH/FLAV and PAC fractions were more effective in promoting microbiome alpha diversity compared to S/A and TPP, and these effects were attributed to differentially responsive taxa. Dietary enrichment with BB resulted in a moderate increase in the diversity of the microbiota of the older subjects but not in younger subjects, and certain health-relevant taxa were significantly associated with BB consumption. Alterations in the abundance of some gut bacteria correlated not only with BB consumption but also with increased antioxidant activity in blood. Collectively, these pilot data support the notion that BB consumption is associated with gut microbiota changes and health benefits.

Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes

Nontypeable Haemophilus influenzae (NTHi) colonizes human upper respiratory airways and plays a key role in the course and pathogenesis of acute exacerbations of chronic obstructive pulmonary disease (COPD). Currently, it is not possible to distinguish COPD isolates of NTHi from other clinical isolates of NTHi using conventional genotyping methods. Here, we analysed the core and accessory genome of 568 NTHi isolates, including 40 newly sequenced isolates, to look for genetic distinctions between NTHi isolates from COPD with respect to other illnesses, including otitis media, meningitis and pneumonia. Phylogenies based on polymorphic sites in the core-genome did not show discrimination between NTHi strains collected from different clinical phenotypes. However, pan-genome-wide association studies identified 79 unique NTHi accessory genes that were significantly associated with COPD. Furthermore, many of the COPD-related NTHi genes have known or predicted roles in virulence, transmembrane transport of metal ions and nutrients, cellular respiration and maintenance of redox homeostasis. This indicates that specific genes may be required by NTHi for its survival or virulence in the COPD lung. These results advance our understanding of the pathogenesis of NTHi infection in COPD lungs.

Planktonic and Sessile Artificial Colonic Microbiota Harbor Distinct Composition and Reestablish Differently upon Frozen and Freeze-Dried Long-Term Storage

Fecal microbiota transplantation has been successfully applied in the treatment of recurrent Clostridium difficile infection and has been suggested as an alternative therapy for other intestinal disorders such as inflammatory bowel disease or metabolic syndrome. “Artificial” colonic microbiota delivered by PolyFermS continuous fermentation models can provide a controllable and reproducible alternative to fecal transplantation, but effective preservation strategies must be developed. In this study, we systematically investigated the response of sessile and planktonic artificial colonic microbiota to cryopreservation and lyophilization. We suggest that functional redundancy is an important factor in providing functional stability with respect to exposure to stress during processing and storage. Functional redundancy in compositionally reduced microbial systems may be considered when designing microbial products for therapy.

Biofilm-associated, sessile communities represent the major bacterial lifestyle, whereas planktonic cells mainly appear during initial colonization of new surfaces. Previous research, mainly performed with pathogens, demonstrated increased environmental stress tolerance of biofilm-growing compared to planktonic bacteria. The lifestyle-specific stress response of colonic microbiota, both natural and fermentation produced, has not been addressed before. Planktonic and sessile “artificial” colonic microbiota delivered by PolyFermS continuous fermentation models can provide a controllable and reproducible alternative to fecal transplantation in treating gastrointestinal disorders. We therefore characterized planktonic and sessile microbiota produced in two PolyFermS models inoculated with immobilized fecal microbiota and comparatively tested their levels of tolerance of frozen storage (–80°C) and freeze-dried storage (4°C) for 9 months to mimic preservation strategies for therapeutic applications. Sessile microbiota harbored next to shared taxa a unique community distinguishable from planktonic microbiota. Synergistetes and Proteobacteria were highly represented in sessile microbiota, while Firmicutes were more abundant in planktonic microbiota. The community structure and metabolic activity of both microbiota, monitored during standardized reactivation batch fermentations, were better preserved after frozen storage than dried storage, indicated by higher Bray-Curtis similarity and enhanced recovery of metabolite production. For both lifestyles, reestablishment of Bacteroidaceae was impaired after frozen and dried storage along with reduced propionate formation. In contrast, butyrate production was maintained after reactivation despite compositional rearrangements within the butyrate-producing community. Unexpectedly, the rate of recovery of metabolite production was lower after preservation of sessile than planktonic microbiota. We speculate that higher functional dependencies between microbes might have led to the lower stress tolerance of sessile than planktonic microbiota.

IMPORTANCE Fecal microbiota transplantation has been successfully applied in the treatment of recurrent Clostridium difficile infection and has been suggested as an alternative therapy for other intestinal disorders such as inflammatory bowel disease or metabolic syndrome. “Artificial” colonic microbiota delivered by PolyFermS continuous fermentation models can provide a controllable and reproducible alternative to fecal transplantation, but effective preservation strategies must be developed. In this study, we systematically investigated the response of sessile and planktonic artificial colonic microbiota to cryopreservation and lyophilization. We suggest that functional redundancy is an important factor in providing functional stability with respect to exposure to stress during processing and storage. Functional redundancy in compositionally reduced microbial systems may be considered when designing microbial products for therapy.

Maximal information transmission is compatible with ultrasensitive biological pathways

Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological systems outputs might feed back into inputs due to cell motility, and the biological channel can change by mutations during evolution. Here, we show that the conventional channel capacity obtained by optimizing the input distribution for a fixed channel may not reflect the global optimum. In a new approach we analytically identify both input distributions and input-output curves that optimally transmit information, given constraints from noise and the dynamic range of the channel. We find a universal optimal input distribution only depending on the input noise, and we generalize our formalism to multiple outputs (or inputs). Applying our formalism to Escherichia coli chemotaxis, we find that its pathway is compatible with optimal information transmission despite the ultrasensitive rotary motors.

Microbes: possible link between modern lifestyle transition and the rise of metabolic syndrome

The rapid decrease in infectious diseases globally has coincided with an increase in the prevalence of obesity and other components of metabolic syndrome. Insulin resistance is a common feature of metabolic syndrome and can be influenced by genetic and non-genetic/environmental factors. The emergence of metabolic syndrome epidemics over only a few decades suggests a more prominent role of the latter. Changes in our environment and lifestyle have indeed paralleled the rise in metabolic syndrome. Gastrointestinal tract microbiota, the composition of which plays a significant role in host physiology, including metabolism and energy homeostasis, are distinctly different within the context of metabolic syndrome. Among humans, recent lifestyle-related changes could be linked to changes in diversity and composition of 'ancient' microbiota. Given the co-adaptation and co-evolution of microbiota with the immune system over a long period of time, it is plausible that such lifestyle-related microbiota changes could trigger aberrant immune responses, thereby predisposing an individual to a variety of diseases. Here, we review current evidence supporting a role for gut microbiota in the ongoing rise of metabolic syndrome. We conclude that population-level shifts in microbiota can play a mediatory role between lifestyle factors and pathogenesis of insulin resistance and metabolic syndrome.

Retention of Microbiota Diversity by Lactose-Free Milk in a Mouse Model of Elderly Gut Microbiota

Prebiotics may improve aging-related dysbiosis. Milk is a source of nutrients including oligosaccharides whose prebiotic potential remains largely unexplored. We used a murine model to explore the effect of milk products on high diversity and lower diversity faecal microbiota from healthy and frail elderly subjects, respectively. Mice were treated with antibiotics and subsequently "humanized" with human faecal microbiota. The mice received lactose-free or whole milk, glycomacropeptide, or soy protein (control) supplemented diets for one month. The faecal microbiota was analyzed by 16S rRNA gene amplicon sequencing. Lactose-free milk diet was as efficient as the control diet in retaining faecal microbiota diversity in mice. Both milk diets had a significant effect on the relative abundance of health-relevant taxa (e.g., Ruminococcaceae, Lachnospiraceae). The glycomacropeptide prebiotic activity previously observed in vitro was not replicated in vivo. However, these data indicate the novel prebiotic potential of bovine milk for human nutrition.

Development and Organization of the Secondary and Tertiary Lymphoid Organs: Influence of Microbial and Food Antigens

Background:

Secondary lymphoid organs (SLO) are distributed in many districts of the body and, especially, lymph nodes, spleen and gut-associated lymphoid tissue are the main cellular sites. On the other hand, tertiary lymphoid organs (TLO) are formed in response to inflammatory, infectious, autoimmune and neoplastic events. </P><P> Developmental Studies: In the present review, emphasis will be placed on the developmental differences of SLO and TLO between small intestine and colon and on the role played by various chemokines and cell receptors. Undoubtedly, microbiota is indispensable for the formation of SLO and its absence leads to their poor formation, thus indicating its strict interaction with immune and non immune host cells. Furthermore, food antigens (for example, tryptophan derivatives, flavonoids and byphenils) bind the aryl hydrocarbon receptor on innate lymphoid cells (ILCs), thus promoting the development of postnatal lymphoid tissues. Also retinoic acid, a metabolite of vitamin A, contributes to SLO development during embryogenesis. Vitamin A deficiency seems to account for reduction of ILCs and scarce formation of solitary lymphoid tissue. </P><P> Translational Studies: The role of lymphoid organs with special reference to intestinal TLO in the course of experimental and human disease will also be discussed. </P><P> Future Perspectives: Finally, a new methodology, the so-called “gut-in-a dish”, which has facilitated the in vitro interaction study between microbe and intestinal immune cells, will be described.

Systems biology approaches in the study of Chinese herbal formulae

Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function. It is the study of the composition of all components of a biological system and their interactions under specific conditions. The core of systems biology is holistic and systematic research, which is different from the manner of thinking and research of all other branches of biology to date. Chinese herbal formulae (CHF) are the main form of Chinese medicine and are composed of single Chinese herbal medicines (CHMs) with pharmacological and pharmacodynamic compatibility. When single CHMs are combined into CHF, the result is different from the original effect of a single drug and can be better adapted to more diseases with complex symptoms. CHF represent a complex system with multiple components, targets and effects. Therefore, the use of systems biology is conducive to revealing the complex characteristics of CHF. With the rapid development of omics technologies, systems biology has been widely and increasingly applied to the study of the basis of the pharmacological substances, action targets and mechanisms of CHF. To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and metagenomics and their applications in research on CHF.

The influence of diet and environment on the gut microbial community of field crickets

The extent to which diet and environment influence gut community membership (presence or absence of taxa) and structure (individual taxon abundance) is the subject of growing interest in microbiome research. Here, we examined the gut bacterial communities of three cricket groups: (1) wild caught field crickets, (2) laboratory-reared crickets fed cat chow, and (3) laboratory-reared crickets fed chemically defined diets. We found that both environment and diet greatly altered the structure of the gut bacterial community. Wild crickets had greater gut microbial diversity and higher Firmicutes to Bacteroidetes ratios, in contrast to laboratory-reared crickets. Predictive metagenomes revealed that laboratory-reared crickets were significantly enriched in amino acid degradation pathways, while wild crickets had a higher relative abundance of peptidases that would aid in amino acid release. Although wild and laboratory animals differ greatly in their bacterial communities, we show that the community proportional membership remains stable from Phylum to Family taxonomic levels regardless of differences in environment and diet, suggesting that endogenous factors, such as host genetics, have greater control in shaping gut community membership.

Immunological roulette: Luck or something more? Considering the connections between host and environment in TB

Accurate prediction of which patient will progress from a sub-clinical Mycobacterium tuberculosis infection to active tuberculosis represents an elusive, yet critical, clinical research objective. From the individual perspective, progression can be considered to be the product of a series of unfortunate events or even a run of bad luck. Here, we identify the subtle physiological relationships that can influence the odds of progression to active TB and how this progression may reflect directed dysbiosis in a number of interrelated systems. Most infected individuals who progress to disease have apparently good immune responses, but these responses are, at times, compromised by either local or systemic environmental factors. Obvious disease promoting processes, such as tissue-damaging granulomata, usually manifest in the lung, but illness is systemic. This apparent dichotomy between local and systemic reflects a clear need to define the factors that promote progression to active disease within the context of the body as a physiological whole. We discuss aspects of the host environment that can impact expression of immunity, including the microbiome, glucocorticoid-mediated regulation, catecholamines and interaction between the gut, liver and lung. We suggest the importance of integrating precision medicine into our analyses of experimental outcomes such that apparently conflicting results are not contentious, but rather reflect the impact of these subtle relationships with our environment and microbiota.