Commentary
Biological Psychiatry
Metagenomics: A New Frontier for Translational Research and Personalized Therapeutics in Psychiatry? Andrew C. Heath Human metagenomics is the genomic study of the microbial communities that inhabit Homo sapiens. Why should biomedical researchers and clinicians whose primary focus is psychiatric disorders, and who typically lack interest and expertise in microbiology, pay attention to a fast-moving literature on metagenomics? The past decade has seen important advances in research, notably concerning the gut microbiome (aggregate collection of gut microbial genomes and genes) which is the focus of the article by Bruce-Keller et al. (1). These advances highlight the potential for new insights into etiology and therapeutics from metagenomics research. The gut microbiome encodes metabolic functions that enable digestion of certain components of human diet (2); it forms at birth and undergoes important changes through the dietary changes of infancy and early childhood as well as under extreme conditions such as malnutrition (3). These advances build on long-established research approaches: the use of gnotobiotic—germ-free (GF)—mice, microbiota transplantation into previously gnotobiotic mice (a gut microbiota is a community of microbes resident in the gut), and family study including twin pair paradigms. These approaches, when used together with next-generation sequencing, provide a very powerful framework for translational research. Emerging basic science and clinical research findings on the gut microbiome and its involvement in obesity and associated metabolic dysfunction include the following: 1) enormous interindividual variability of the human microbiome (4,5) but with evidence for sibling (twin pair) resemblance that persists even in adulthood (5) as well as for high intraindividual long-term stability in adults (6), 2) evidence that the human physiologic state of obesity is associated with a loss of gut microbial diversity that may be hypothesized to play a role in sustaining obesity (5,7), 3) demonstration that human-tomouse gut microbiota transplantation using fecal samples from obese versus lean human donors (selected from obesity-discordant twin pairs) can transmit differences in adiposity as well as metabolomics features previously noted to be associated with human obesity-associated metabolic dysfunction (insulin resistance) (7), and 4) evidence using this “humanized” mouse model that the combination of microbial replacement and “good diet” may prevent adiposity gain and associated metabolomics indicators of metabolic dysfunction (7). Although the greatest progress has been made on obesity, these advances should have much broader applicability to conditions where disruption of the gut microbiota may be expected (e.g., alcoholism, eating disorders). The findings reported by Bruce-Keller et al. (1) suggest that these advances may be more broadly useful in psychiatry in understanding
mechanisms underlying associations of obesity with disorders such as major depression and neuroinflammation and cognitive dysfunction. Bruce-Keller et al. (1) conclude with the potential for pharmacologic or dietary therapy to improve obesity-associated neurologic outcomes, whereas work on obesity and the gut microbiome suggests the ultimate potential for a combination diet and microbial replacement therapy. Key progress in research on the gut microbiome and obesity began with a C57BL/6J mouse model and a hypothesis about Homo sapiens, including an observation that adult GF mice raised in sterile conditions in an isolator, when inoculated with the gut microbiota of conventionally reared (CONV-R) mice, show a rapid increase in body fat despite reduced food intake; an investigation of underlying mechanisms; and the hypothesis that the microbiota of obese individuals has increased efficiency in extracting energy from food (8). Because GF mice lack certain metabolic functions normally carried out by the gut microbiota, they are malnourished compared with CONV-R mice, making direct interpretation of behavioral differences between GF versus CONV-R mice problematic. However, Turnbaugh et al. (2) combined a mouse genetic model of obesity (homozygous ob/ob mice who are leptin deficient, contrasted with ob/1 heterozygous and 1/1 wild-type littermates) with microbiota transplantation into wild-type GF mice. Previously, these investigators had shown a host genotype effect on gut microbiota composition, with marked differences in relative abundance of the two most common divisions (in mice and humans) of Bacteria, Bacteroidetes and Firmicutes, in ob/ob mice compared with littermate control mice, with 50% increase of the former and decrease of the latter. By transplantation of the cecal microbiota of ob/ob versus 1/1 donors into 1/1 GF recipients, they were able to show not only that, consistent with donor differences, ob/ob microbiota recipients had increased abundance of Firmicutes compared with leandonor microbiota recipients but also that, despite no differences in initial weight or body fat or in chow consumption, ob/ob microbiota recipients showed a significantly greater percentage increase in body fat. Subsequent work showed the transmissibility of an adiposity phenotype as a function of diet-induced obesity in the donor mice (9). Bruce-Keller et al. (1) set out to test, in mice, the hypothesis that effects of a high-fat diet on gut microbial composition may contribute to previously reported associations in the literature between obesity and both psychiatric disorders (e.g., major depression) and cognitive dysfunction. Given the many potentially interacting confounders in these relationships (e.g., low socioeconomic level, smoking) in humans, there is a strong case for wanting to address these questions using
SEE CORRESPONDING ARTICLE ON PAGE 607 & 2015 Society of Biological Psychiatry Biological Psychiatry April 1, 2015; 77:600–601 www.sobp.org/journal
600
ISSN: 0006-3223
Biological Psychiatry
Commentary
animal models. The authors use microbiota transplantation from mouse donors fed a high-fat diet versus control donors. Their article has some limitations, as follows. The authors use an antibiotic regimen to approximate GF status in their microbiota recipient mice (with imperfect success) before transplantation; their primary behavioral tests are measures of anxiety, whereas the clinical literature emphasizes associations of obesity and related conditions with major depression; they emphasize no differences in body weight between highfat diet and healthy diet microbiota recipients that could influence their findings, whereas prior research emphasized body fat outcome; and they report no differences in metabolic dysfunction between recipient groups, without confirmation by metabolomics analysis, although more recent research (using human donors with mouse recipients) found differences in metabolomics profile in recipient mice consistent with the differences observed in insulin-resistant humans, in the absence of gross metabolic abnormalities (7). Nonetheless, the basic findings of Bruce-Keller et al.—of more anxiety-like behaviors in recipients of a high-fat microbiota than control subjects and increased evidence for neuroinflammation—if replicated, are of considerable importance. Where do we go from here? Perhaps it is time to move on to research including obese humans. Bruce-Keller et al. (1) emphasize that they do not find major differences as a function of diet condition at the level of Bacteroidetes versus Firmicutes (which also now appears to be the case for human obesity differences (5)) and rather report differences at the level of Bacteria. Turnbaugh et al. (10), motivated by the challenge that the CONV-R mouse gut microbiota is not a good model for the human gut microbiota, used shotgun sequencing to establish successful recapture of the human gut microbiota, sampled from either fresh or frozen stool, after transplant into GF mice maintained in an isolator, creating a “humanized” model with the gut microbiota of a specific human donor. This has proved to be an extraordinarily fruitful insight, especially when combined with a further insight from the laboratory of the same senior investigator that experiments using cohousing of GF mouse pairs who were recipients of transplants from twin pair donors who were discordant for a condition or disorder that affected gut microbial composition (e.g., obesity (7)) could advance understanding of patterns of microbial loss and the potential and conditions for success for microbial replacement therapy. Turning to humans, Turnbaugh et al. (5) used fecal samples from stably concordant lean twin pairs (body mass index [BMI] of both twins 18.5–24.9 across multiple waves of assessment) and concordant obese pairs (both BMI $ 30 and in many cases BMI $ 35) to address the state of the human gut microbiota in obesity; a major finding was reduced gut microbial diversity in individuals from concordant obese pairs. The follow-up article by Ridaura et al. (7) used fecal samples from rare twin pairs (n 5 4) who were discordant lean/obese to create lean-donor and obese-donor mice. These investigators confirmed transmission of an adiposity phenotype and associated metabolomics abnormalities, whether using uncultured or cultured microbiota for transplantation, with good recapture of the taxonomic features of the human donor’s microbiota and of the functions encoded by the donor’s microbiome. Mice are coprophagic (i.e., will eat each other’s feces), and
cohousing provides a natural mechanism for mouse-to-mouse transfer of gut microbes. Ridaura et al. (7) found that when leandonor and obese-donor mice, created using sibling donors, were cohoused under conditions of laboratory chow or low-fat (but not high-fat) diet, the adiposity gain in the obese-donor mice was prevented, with an accompanying asymmetric pattern of microbial invasion from the obese-donor to the lean-donor mice. A straightforward interpretation—because twin pairs would be expected to begin life with very similar gut microbiotas—is that there has been a loss of microbial diversity in the obese twin, with the loss of critical microbes remediated via mouse-to-mouse transfer from the lean-donor to obese-donor mice. If confirmed, this interpretation would set the stage for continuing research to identify gut microbes whose loss (and replacement) may play a role in sustaining (and overcoming) obesity and its adverse consequences. The combination of dietary and microbial replacement therapy ultimately may play a role in psychiatric personalized medicine.
Acknowledgments and Disclosures This work was supported by National Institutes of Health Grant Nos. P01 DK078669 and K05 AA017688. The author reports no biomedical financial interests or potential conflicts of interest.
Article Information From the Alcoholism Research Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri. Address correspondence to Andrew C. Heath, D.Phil., Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid, CB 8134, St. Louis, MO 63110; E-mail: [email protected]. Received and accepted Jan 30, 2015.
References 1.
2.
3.
4. 5.
6.
7.
8.
9.
10.
Bruce-Keller AJ, Salbaum JM, Luo M, Blanchard E 4th, Taylor CM, Welsh DA, et al. (2015): Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol Psychiatry 77:607–615. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006): An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, et al. (2013): Meta-analyses of studies of the human microbiota. Genome Res 23:1704–1714. Human Microbiome Project Consortium (2012): Structure, function and diversity of the healthy human microbiome. Nature 486:207–214. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. (2009): A core gut microbiome in obese and lean twins. Nature 457:480–484. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. (2013): The long-term stability of the human gut microbiota. Science 341:1237439. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. (2013): Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341:1241214. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. (2004): The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101:15718–15723. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI (2008): Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213–223. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009): The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: 6ra14.
Biological Psychiatry April 1, 2015; 77:600–601 www.sobp.org/journal
601
Biological Psychiatry
Metagenomics: A New Frontier for Translational Research and Personalized Therapeutics in Psychiatry? Andrew C. Heath Human metagenomics is the genomic study of the microbial communities that inhabit Homo sapiens. Why should biomedical researchers and clinicians whose primary focus is psychiatric disorders, and who typically lack interest and expertise in microbiology, pay attention to a fast-moving literature on metagenomics? The past decade has seen important advances in research, notably concerning the gut microbiome (aggregate collection of gut microbial genomes and genes) which is the focus of the article by Bruce-Keller et al. (1). These advances highlight the potential for new insights into etiology and therapeutics from metagenomics research. The gut microbiome encodes metabolic functions that enable digestion of certain components of human diet (2); it forms at birth and undergoes important changes through the dietary changes of infancy and early childhood as well as under extreme conditions such as malnutrition (3). These advances build on long-established research approaches: the use of gnotobiotic—germ-free (GF)—mice, microbiota transplantation into previously gnotobiotic mice (a gut microbiota is a community of microbes resident in the gut), and family study including twin pair paradigms. These approaches, when used together with next-generation sequencing, provide a very powerful framework for translational research. Emerging basic science and clinical research findings on the gut microbiome and its involvement in obesity and associated metabolic dysfunction include the following: 1) enormous interindividual variability of the human microbiome (4,5) but with evidence for sibling (twin pair) resemblance that persists even in adulthood (5) as well as for high intraindividual long-term stability in adults (6), 2) evidence that the human physiologic state of obesity is associated with a loss of gut microbial diversity that may be hypothesized to play a role in sustaining obesity (5,7), 3) demonstration that human-tomouse gut microbiota transplantation using fecal samples from obese versus lean human donors (selected from obesity-discordant twin pairs) can transmit differences in adiposity as well as metabolomics features previously noted to be associated with human obesity-associated metabolic dysfunction (insulin resistance) (7), and 4) evidence using this “humanized” mouse model that the combination of microbial replacement and “good diet” may prevent adiposity gain and associated metabolomics indicators of metabolic dysfunction (7). Although the greatest progress has been made on obesity, these advances should have much broader applicability to conditions where disruption of the gut microbiota may be expected (e.g., alcoholism, eating disorders). The findings reported by Bruce-Keller et al. (1) suggest that these advances may be more broadly useful in psychiatry in understanding
mechanisms underlying associations of obesity with disorders such as major depression and neuroinflammation and cognitive dysfunction. Bruce-Keller et al. (1) conclude with the potential for pharmacologic or dietary therapy to improve obesity-associated neurologic outcomes, whereas work on obesity and the gut microbiome suggests the ultimate potential for a combination diet and microbial replacement therapy. Key progress in research on the gut microbiome and obesity began with a C57BL/6J mouse model and a hypothesis about Homo sapiens, including an observation that adult GF mice raised in sterile conditions in an isolator, when inoculated with the gut microbiota of conventionally reared (CONV-R) mice, show a rapid increase in body fat despite reduced food intake; an investigation of underlying mechanisms; and the hypothesis that the microbiota of obese individuals has increased efficiency in extracting energy from food (8). Because GF mice lack certain metabolic functions normally carried out by the gut microbiota, they are malnourished compared with CONV-R mice, making direct interpretation of behavioral differences between GF versus CONV-R mice problematic. However, Turnbaugh et al. (2) combined a mouse genetic model of obesity (homozygous ob/ob mice who are leptin deficient, contrasted with ob/1 heterozygous and 1/1 wild-type littermates) with microbiota transplantation into wild-type GF mice. Previously, these investigators had shown a host genotype effect on gut microbiota composition, with marked differences in relative abundance of the two most common divisions (in mice and humans) of Bacteria, Bacteroidetes and Firmicutes, in ob/ob mice compared with littermate control mice, with 50% increase of the former and decrease of the latter. By transplantation of the cecal microbiota of ob/ob versus 1/1 donors into 1/1 GF recipients, they were able to show not only that, consistent with donor differences, ob/ob microbiota recipients had increased abundance of Firmicutes compared with leandonor microbiota recipients but also that, despite no differences in initial weight or body fat or in chow consumption, ob/ob microbiota recipients showed a significantly greater percentage increase in body fat. Subsequent work showed the transmissibility of an adiposity phenotype as a function of diet-induced obesity in the donor mice (9). Bruce-Keller et al. (1) set out to test, in mice, the hypothesis that effects of a high-fat diet on gut microbial composition may contribute to previously reported associations in the literature between obesity and both psychiatric disorders (e.g., major depression) and cognitive dysfunction. Given the many potentially interacting confounders in these relationships (e.g., low socioeconomic level, smoking) in humans, there is a strong case for wanting to address these questions using
SEE CORRESPONDING ARTICLE ON PAGE 607 & 2015 Society of Biological Psychiatry Biological Psychiatry April 1, 2015; 77:600–601 www.sobp.org/journal
600
ISSN: 0006-3223
Biological Psychiatry
Commentary
animal models. The authors use microbiota transplantation from mouse donors fed a high-fat diet versus control donors. Their article has some limitations, as follows. The authors use an antibiotic regimen to approximate GF status in their microbiota recipient mice (with imperfect success) before transplantation; their primary behavioral tests are measures of anxiety, whereas the clinical literature emphasizes associations of obesity and related conditions with major depression; they emphasize no differences in body weight between highfat diet and healthy diet microbiota recipients that could influence their findings, whereas prior research emphasized body fat outcome; and they report no differences in metabolic dysfunction between recipient groups, without confirmation by metabolomics analysis, although more recent research (using human donors with mouse recipients) found differences in metabolomics profile in recipient mice consistent with the differences observed in insulin-resistant humans, in the absence of gross metabolic abnormalities (7). Nonetheless, the basic findings of Bruce-Keller et al.—of more anxiety-like behaviors in recipients of a high-fat microbiota than control subjects and increased evidence for neuroinflammation—if replicated, are of considerable importance. Where do we go from here? Perhaps it is time to move on to research including obese humans. Bruce-Keller et al. (1) emphasize that they do not find major differences as a function of diet condition at the level of Bacteroidetes versus Firmicutes (which also now appears to be the case for human obesity differences (5)) and rather report differences at the level of Bacteria. Turnbaugh et al. (10), motivated by the challenge that the CONV-R mouse gut microbiota is not a good model for the human gut microbiota, used shotgun sequencing to establish successful recapture of the human gut microbiota, sampled from either fresh or frozen stool, after transplant into GF mice maintained in an isolator, creating a “humanized” model with the gut microbiota of a specific human donor. This has proved to be an extraordinarily fruitful insight, especially when combined with a further insight from the laboratory of the same senior investigator that experiments using cohousing of GF mouse pairs who were recipients of transplants from twin pair donors who were discordant for a condition or disorder that affected gut microbial composition (e.g., obesity (7)) could advance understanding of patterns of microbial loss and the potential and conditions for success for microbial replacement therapy. Turning to humans, Turnbaugh et al. (5) used fecal samples from stably concordant lean twin pairs (body mass index [BMI] of both twins 18.5–24.9 across multiple waves of assessment) and concordant obese pairs (both BMI $ 30 and in many cases BMI $ 35) to address the state of the human gut microbiota in obesity; a major finding was reduced gut microbial diversity in individuals from concordant obese pairs. The follow-up article by Ridaura et al. (7) used fecal samples from rare twin pairs (n 5 4) who were discordant lean/obese to create lean-donor and obese-donor mice. These investigators confirmed transmission of an adiposity phenotype and associated metabolomics abnormalities, whether using uncultured or cultured microbiota for transplantation, with good recapture of the taxonomic features of the human donor’s microbiota and of the functions encoded by the donor’s microbiome. Mice are coprophagic (i.e., will eat each other’s feces), and
cohousing provides a natural mechanism for mouse-to-mouse transfer of gut microbes. Ridaura et al. (7) found that when leandonor and obese-donor mice, created using sibling donors, were cohoused under conditions of laboratory chow or low-fat (but not high-fat) diet, the adiposity gain in the obese-donor mice was prevented, with an accompanying asymmetric pattern of microbial invasion from the obese-donor to the lean-donor mice. A straightforward interpretation—because twin pairs would be expected to begin life with very similar gut microbiotas—is that there has been a loss of microbial diversity in the obese twin, with the loss of critical microbes remediated via mouse-to-mouse transfer from the lean-donor to obese-donor mice. If confirmed, this interpretation would set the stage for continuing research to identify gut microbes whose loss (and replacement) may play a role in sustaining (and overcoming) obesity and its adverse consequences. The combination of dietary and microbial replacement therapy ultimately may play a role in psychiatric personalized medicine.
Acknowledgments and Disclosures This work was supported by National Institutes of Health Grant Nos. P01 DK078669 and K05 AA017688. The author reports no biomedical financial interests or potential conflicts of interest.
Article Information From the Alcoholism Research Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri. Address correspondence to Andrew C. Heath, D.Phil., Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid, CB 8134, St. Louis, MO 63110; E-mail: [email protected]. Received and accepted Jan 30, 2015.
References 1.
2.
3.
4. 5.
6.
7.
8.
9.
10.
Bruce-Keller AJ, Salbaum JM, Luo M, Blanchard E 4th, Taylor CM, Welsh DA, et al. (2015): Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol Psychiatry 77:607–615. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006): An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, et al. (2013): Meta-analyses of studies of the human microbiota. Genome Res 23:1704–1714. Human Microbiome Project Consortium (2012): Structure, function and diversity of the healthy human microbiome. Nature 486:207–214. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. (2009): A core gut microbiome in obese and lean twins. Nature 457:480–484. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. (2013): The long-term stability of the human gut microbiota. Science 341:1237439. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. (2013): Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341:1241214. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. (2004): The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101:15718–15723. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI (2008): Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213–223. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009): The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: 6ra14.
Biological Psychiatry April 1, 2015; 77:600–601 www.sobp.org/journal
601
