Determinants of Microbial Antibiotic Susceptibility: The Commensal Gut Microbiota Perspective
Authors: Jacob E. Moskowitz, Suzanne Devkota
Journal: Cell Host & Microbe (2019)

Ng et al., 2019Ng K.M. Aranda-Diaz A. Tropini C. Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs.Cell Host Microbe. 2019; 26 (this issue): 650-665Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar unravel the complex factors that shape commensal gut microbiota susceptibility and resilience to antibiotics. These findings depict the microbiota’s malleable dynamics resulting from compositional changes, environmental variability, and dietary shifts, further informing potential strategies to mitigate incomplete microbiome recovery accompanying antibiotic treatment. Ng et al., 2019Ng K.M. Aranda-Diaz A. Tropini C. Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs.Cell Host Microbe. 2019; 26 (this issue): 650-665Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar unravel the complex factors that shape commensal gut microbiota susceptibility and resilience to antibiotics. These findings depict the microbiota’s malleable dynamics resulting from compositional changes, environmental variability, and dietary shifts, further informing potential strategies to mitigate incomplete microbiome recovery accompanying antibiotic treatment. Mammals have co-evolved with complex microbial ecosystems from time immemorial, and the highest bacterial densities have been present in the lower gastrointestinal tract. The prevalence of diverse microbial pathogens capable of causing infectious disease spurred the development of a wide variety of antibiotics. However, ecological studies of the gut microbiome over the past decade (Dethlefsen and Relman, 2011Dethlefsen L. Relman D.A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.Proc. Natl. Acad. Sci. USA. 2011; 108: 4554-4561Crossref PubMed Scopus (1534) Google Scholar) have made it apparent that these advances in modern medicine brought with them a robust capacity to disrupt the host-microbe co-evolutionary relationship upon which we so strongly rely. In the current study, Ng et al., 2019Ng K.M. Aranda-Diaz A. Tropini C. Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs.Cell Host Microbe. 2019; 26 (this issue): 650-665Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar longitudinally characterize commensal microbial dynamics during and after treatment with antibiotics, but they also delve into the extrinsic factors, such as diet and environmental reservoirs, that could shape and determine resilience. This endeavor is particularly timely given the recent debates regarding the efficacy of probiotics for restoring the gut microbiota after the use of antibiotics. Are there better recovery strategies that leverage the natural environment of the host? Indeed, the growing threat of pathogenic antibiotic resistance has encouraged persistent efforts to uncover mechanisms of resistance and therapeutic strategies to overcome superinfections. Though these efforts continue to gain traction, our understanding of commensal gut microbiota responses to antibiotics remains limited despite intimate associations between gut microbiota deviations and various health consequences. Elucidating underlying factors that drive microbiota responses in human populations presents a formidable challenge because studies are hampered by substantial variability across people and places. This observation invites us to question how varying initial gut microbiota communities might direct a particular response to antibiotics and further necessitates the use of animal models in standardized conditions to address the role of individual factors. In studies incorporating animal models, antibiotic cocktails are frequently used to create minimal intestinal microbiotas for the study of host-microbial interactions in a specific context (Josefsdottir et al., 2017Josefsdottir K.S. Baldridge M.T. Kadmon C.S. King K.Y. Antibiotics impair murine hematopoiesis by depleting the intestinal microbiota.Blood. 2017; 129: 729-739Crossref PubMed Scopus (158) Google Scholar, Lamousé-Smith et al., 2011Lamousé-Smith E.S. Tzeng A. Starnbach M.N. The intestinal flora is required to support antibody responses to systemic immunization in infant and germ free mice.PLoS One. 2011; 6: e27662Crossref PubMed Scopus (64) Google Scholar). This use of antibiotics as tools themselves demonstrates their profound capacity to disrupt the gut microbiota. However, gut microbiota responses to a given antibiotic, even under controlled experimental conditions, are reportedly inconsistent (Ng et al., 2019Ng K.M. Aranda-Diaz A. Tropini C. Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs.Cell Host Microbe. 2019; 26 (this issue): 650-665Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar). This suggests that other unknown environmental or circumstantial factors are also at play. We know that diet is intimately associated with the commensal gut microbiota through various mechanisms. For example, the removal of microbiota-accessible carbohydrates (MACs), i.e., dietary fiber, results in a compositional shift of the gut microbiota and leads to subsequent changes in the protective mucus barrier (Desai et al., 2016Desai M.S. Seekatz A.M. Koropatkin N.M. Kamada N. Hickey C.A. Wolter M. Pudlo N.A. Kitamoto S. Terrapon N. Muller A. et al.A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility.Cell. 2016; 167: 1339-1353.e21Abstract Full Text Full Text PDF PubMed Scopus (1324) Google Scholar). Given that the mucus layer constitutes an important part of the intestinal-barrier physiology that regulates host exposure to luminal antigens, it will be important to understand how diet might interact with antibiotics and thus influence microbiota response and resilience. Finally, environmental exposures—where you live and with whom you come in contact—most likely have an important role in both the nature and degree of community recovery following a course of antibiotics. It stands to reason that during a time of reduced diversity following exposure, vacated niches can be filled through exposure to environmental reservoirs that dictate community recovery. It is of further interest to understand how variations in microbiota recovery determine community responses to subsequent antibiotic exposure and thereby shape long-term effects of antibiotics. To unravel the complex forces that drive these community dynamics, the authors describe a systematic investigation incorporating humanized and conventionalized gut microbiotas in mice to map the response and recovery of the commensal microbiota. For initial characterization of community responses to antibiotics, the authors colonized germ-free mice with a human stool microbiota that was then treated with a course of either streptomycin or ciprofloxacin. Expectedly, regardless of the antibiotic, fecal bacterial loads were dramatically reduced almost immediately after the start of treatment. Surprisingly, however, bacterial loads recovered quickly while still receiving antibiotics, demonstrating resilience even in the face of continued antibiotic exposure (Figure 1A). Nevertheless, the mice sustained a long-term loss in microbial diversity after recovery. The prominent phylum Bacteroidetes was specifically suppressed regardless of antibiotic choice both during and after treatment, whereas the Firmicutes phylum was minimally affected and primarily occupied the vacated niche as a result of Bacteroidetes loss. Interestingly, a single Bacteroidetes member, Bacteroides vulgatus (Bv), transiently bloomed and was largely responsible for the recovery of Bacteroidetes after ciprofloxacin treatment (Figure 1A). The Bv dominance coinciding with extinction of other taxa within Bacteroidaceae led the authors to hypothesize that the Bacteroidaceae family and the gut microbiota community as a whole experience selection for resilience during recovery from initial ciprofloxacin treatment. Remarkably, pre-antibiotic Bacteroides isolates demonstrated susceptibility to ciprofloxacin in vitro, consistent with the literature, whereas the dominant Bv isolates collected after initial treatment had greater than 100-fold increased resistance to ciprofloxacin. Further sequencing analysis revealed that, in the gyrA gene, the dominant Bv isolates had acquired a mutation known to confer resistance to ciprofloxacin. To further test the dynamics of both in vitro and in vivo Bacteroides susceptibility, the authors tested laboratory Bacteroides strains for resistance to streptomycin. As seen in previous in vitro studies, these strains were resistant to streptomycin at extremely high doses. However, there was a dramatic decrease in the relative abundance of Bacteroides after mice were treated with the antibiotic, indicating in vivo susceptibility. These results highlight the stark contrast in Bacteroides dynamics between in vitro and in vivo systems and demonstrate that in vitro testing fails to account for bacterial responses within a complex intestinal ecosystem and furthermore does not consider the potential for rapid accumulation of mutations conferring resistance. Interestingly, antibiotic susceptibility was not consistent across different initial microbiotas. Whereas ciprofloxacin treatment in the humanized gut microbiota selected for resistant Bv, no selection was observed when the experiment was repeated in mice with the microbiota of a conventionalized laboratory mouse. Therefore, we must consider that distinct initial microbiotas contain variable ranges of susceptibility and thus allow for selection to occur during antibiotic treatment in some cases, but not in others. Additional variables such as dietary composition and environmental exposures further interact with the host to shape microbiota response and recovery to antibiotics. To address this, the authors explored whether fiber-deficient diets or single housing would affect recovery of the commensal microbiota after antibiotics. Indeed, they found that both of these conditions, compared with fiber-replete diets and co-housing, resulted in more pronounced loss of diversity and delayed and incomplete recovery of the microbiota (Figure 1B). One explanation for the dietary effects is that the loss of carbohydrate availability confers a competitive advantage for other taxa that can acquire energy by alternative means. Here, it is suggested that the Verrucomicrobiaceae family outcompetes Bacteroidaceae during recovery because of its capacity to use intestinally derived mucins as an alternative carbohydrate source. Thus, dietary factors can profoundly affect microbiota resilience to antibiotics by redirecting competitive advantages within the ecosystem. These data further support the need for an individualized approach toward developing safe and efficient antibiotic-based therapeutic strategies that take into account diet and natural bacterial reservoirs. The present study thoroughly investigates complex determinants of dynamic commensal gut microbiota responses to antibiotics. In doing so, the authors raise a number of interesting questions concerning our approaches to both experimental and clinical antibiotic use. Namely, gut microbiota abundance, but not diversity, following antibiotic treatment occurs much more quickly than previously anticipated. This suggests the need for high-frequency sampling during treatment experiments to avoid missing primary changes. Rapid evolution of the microbiota landscape after external perturbance could therefore explain much of the reproducibility pitfalls currently plaguing these types of studies. Although there appears to be prompt recovery, an extended loss of gut microbiota diversity potentially contributes to antibiotic-associated diseases. Perhaps most striking, this work demonstrates the shortcomings of using in vitro sensitivity testing to inform clinical decisions regarding appropriate antibiotics. However, it must be noted that in vitro responses to antibiotics of known pathogenic organisms have been characterized for nearly a century, whereas we are only beginning to consider this for commensals. As demonstrated by the Bacteroides genus, antibiotic sensitivity of individual taxa could change drastically in the context of the complex gastrointestinal ecosystem. These contextual interactions would ideally be an important consideration in choosing appropriate antibiotics for clinical use. In addition to being complicated by internal host factors that modify community and taxa dynamics, microbiota resiliency is further complicated by external factors such as dietary composition and exposure to environmental microbial reservoirs. Altogether, this wealth of information supports a personalized approach to understanding host-microbe interactions in the context of antibiotics and empowers new strategies to alleviate incomplete recovery of the intestinal microbiota. Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental ReservoirsNg et al.Cell Host & MicrobeNovember 13, 2019In BriefNg et al. systematically compare microbiota responses to antibiotics in mice. A fiber-deficient diet or single housing aggravated otherwise rapid recovery, whereas microbiota reprogramming through repeated treatment or transmission between hosts enhanced resilience. This work highlights the translational potential for modulating diet, sanitation, and microbiota composition during antibiotic treatment. Full-Text PDF Open Archive