Straight From the Gut

  Dirty business: gut transplants give bacteria and scientists new choices. S tephanie is the first to admit that she never had the guts for life. She was born with familial adenomatous polyposis,a genetic disorder in which thousandsof polyps form in the colon. By the age of 22,much of the organ had to be removed. Fouryears later, a massive benign tumour chokedoff the blood supply to her small intestine, sodoctors cut out all but a metre of it. For the next six years, she was fed by a tube every nightuntil the feeding left her liver badly scarred and fighting recurring infections. “I was given a month to live,” she says. That’s when doctors referred Stephanie toGeorgetown University Hospital in Washing- ton DC. There, on 17 April 2006 , surgeons cut out her stomach and what was left of her small and large intestine and replaced it with new organs from a donor who had died days earlier in Tennessee. “Oesophagus to anus, her entire gastrointestinal tract was in the garbage can,”says Tom Fishbein, who directed the surgery. “She got a brand new one.” All organ transplants are complicated,but there are only a handful of centres in theUnited States that have theexpertise to transplanta small intestine, theseven metres of coiled tissue connected up to the stomach at one end and the large intestine at the other. The technique is complicated because the gut is teeming with trillions of bac- teria and other microbes, plus the bulk of thebody’s lymphocytes. Before such transplants, the donor’s intestine has normally been flushed with antibiotics. But rates of infection andrejection from such transplants are very high because, it is thought, some for-eign bacteria and immune cells survive the cleaning process and are thrust into an immuno- suppressed recipient. The idea that these intes-tinal bacteria are a menace isnow under review. By team-ing up with microbiologists, the surgeons aretaking advantage of a rare chance to study microbes as they colonize the walls of the gutafter transplanting an intestine: which onesarrive first, and how they restore the ravaged microbial communities. “An all new ecosystem of organisms had to populate that bowel from scratch,” says Fishbein. Their new appreciationof that ecosystem, along with their grow- ing surgical experience, suggeststhat the populations mightbe better left intact before a transplant. The same studies may  also offer insight into how the gut is first populated by microbes afterbirth, how it recovers from the damage done by a heavy course of antibiotics and, perhaps, how to minimize that damage. “Most people study  this in animal models, but this is a real-person model,” says Brett Finlay, a microbiologist at the University of British Columbia in Vancou-  ver, Canada. “It’s an artificial system in some sense, but it’s a neat model.” How the moist, pink intesti- nal tubing lives in such harmo-nious contact with bacteria has puzzled scientists for decades.But “it’s hard to get in there,especially in a healthy person”, says David Relman, who studiesmicrobiology and immunology  at Stanford University, California. “And to do it in a way that doesn’t perturb the system, and to do it every week or every day, well, forget it.” For this reason, most researchers interested in the contents of human innards have had to collect and filter faeces. Beautiful opportunity The transplant scenario is a unique and attrac- tive alternative. For the first few months afteran operation, the end of the gut that wouldnormally go into the rectum is left poking out of the abdomen   so that doctors can check the transplant is stable. As often as necessary,doctors can probe this stoma, or opening, STRAIGHT FROM THE GUT     T .    F    I    S    H    B    E    I    N “Oesophagus to anus,her entire gastro-intestinal tract was inthe garbage can.” — Tom Fishbein 581 NATURE | Vol 453 | 29 May 2008   HUMAN MICROBIOME   NEWS FEATURE  with an endoscope to pinch off biopsies of the intestinal wall with its microbial community  intact. Yellow faeces and glistening, pink skin are signs that the new intestine has success- fully taken. “That is beautiful stuff,” says Stuart Kaufman, medical director of the intestinal-transplantation programme at Georgetown. “We live for poop like this.”The adult samples are also beautiful stuff for researchers who want to chart the arrivals of the different bacterial species. The material is put on ice and shipped to the lab of Jonathan Eisen, a microbial geneticist at the University of Cali- fornia, Davis. There, graduate student Amber Hartman identifies the inhabitants by analysingdistinguishing gene sequences that vary slightly  between different species of bacteria. It’s far too early to draw firm conclusions from their data; Fishbein and his collaborators haveonly studied 15 patients over the past 2 years.But what they have found suggests that the gutis populated first by enterobacteriaceae, a large family of facultative anaerobes, which can grow with or without oxygen. This suggests that thetransplanted tissue has higher oxygen levelsthan the normal gut, where anaerobic bacteria dominate. Inflammation may boost oxygen lev- els, giving enterobacteria the advantage. Hartman and Eisen have also found thateach person studied so far has had differentproportions of the various microbial species,and that these oscillate rapidly in the first fewmonths after a transplant. Their preliminary  observations suggest that the more chaotic the  variations over time, the worse the outcome of  the transplant. “One thing that becomes very  obvious is that the amount or degree of fluctua-tion is much greater in the sicker patient,” Hart-man says. They now want to know whether the microbiota becomes more stable and reachesequilibrium as a patient recovers, but thatrequires following more patientsover longer times, and intestinal transplants are rare. A different bloody, messy procedure arrives all toooften though: a birth. Here,too, researchers see a fascinat-ing opportunity to explore howmicrobes colonize a gut, onethought to be sterile inside thewomb. During birth and in the hours after, babies can swallow bacteria from the mother’s birth canal, faeces and fromwhatever environment they arrive in. No one knows yet whether bacteria move into a baby’s spanking new innards in the sameway they grab a foothold in a used, adult trans- plant. Much of what scientists know about theformer process has been learned from a study  of Relman’s, in which he and his colleagues col- lected used nappies from 14 babies beginningwith the first stool after birth and at regular intervals throughout the first year of life 1 . What they found mirrored some of the discoveriesin the transplanted intestines: every baby’s microbiota is unique but dynamic, with differ- ent populations of bacterial species shifting in abundance. And as in the transplant study, the babies showed a succession of colonization, with facultative bacteria settling in first, followed by  a more complex and diverse population. Nice and dirty Whatever parallels may emerge from thesestudies, there is one obvious difference: the transplanted gut has already been soiled by the faeces, microbes and immune cells it hosted before. And, until recently, doctors did all they  could to scour away the muck. Paradoxically, the surgeons at Georgetownbegan to notice that the more antibiotics they used to keep the microbes to a minimum, themore intestinal infections they saw after thetransplant. At first, the alterna- tive seemed too fantastic to con- template: taking an essentially infected organ and placing it in a body crippled by immunosup- pressant drugs. But about a yearago, Georgetown and other centres began shifting their practice to do exactly that. Early  evidence indicates that those who receive a gut replete with its native microbiota have fewer chaotic fluctuations. That makes sense in retrospect, notes Eisen, because people who need transplants may do so precisely because they had trouble coloniz- ing their bowels properly to begin with. Insome patients — those with Crohn’s diseaseor ulcerative colitis, for example — the nativebacteria may turn on the body, inflaming thegut and scarring the intestinal walls. So the new intestine might be more likely to help if it comes with its own set of inhabitants. “To take out all the microbes seems completely inane,” Eisen says. The Georgetown researchers have nowstarted to investigate how those bacterialfluctuations during colonization are control-led. They suspect that a gene called NOD2 ,which is expressed in some immune cells, is essential for keeping the chaos to a minimum. The NOD2 protein recognizes components of  bacterial cell walls and controls the production of defensins, small proteins that kill particularbacterial species. The team has found that about 35% of theirtransplant patients carry mutations in NOD2 ,regardless of the intestinal disorder, and thatthose with mutations are 100-fold more likely to have a failed transplant compared with con-trols 2 . The hypothesis is that this mutation somehow lowers production of defensins, so theimmune system is unable to maintain the appro- priate proportions of bacterial species. Perhaps patients with a mutant NOD2 gene might benefitfrom doses of the bacteria that they are missing. In one patient with a NOD2 mutation who later died, “the proportions of normalness were very,  very off”, Hartman says. Quite what ‘off’ is, is hard to define. Theteam still has only a cursory understandingof what the microbiota looks like in healthy  people, compared with their subjects. “It’s like watching colonization of a disturbed ecosys-tem without knowing what was srcinally inthe forest,” says Eisen. That may be helpedby the National Institutes of Health’s HumanMicrobiome Project and other new researchefforts that aim to catalogue the microbes in the human body (see page 578). “We need that field guide to microbes to understand when something is not normal,” Eisen says. In the meantime, clinical signs are still thebest predictors of a transplant’ssuccess. Two years after a newgut was slotted into Stephanie’sbody, she still has scars criss- crossing her abdomen but she is a healthy weight and eats whatever she wants. It is still not clear which microbesto thank: the donor’s bugs that survived frombefore the transplantation, or new microbesthat settled there afterwards. “Whoever’smicrobes have prevailed, they’re probably  good ones,” says Fishbein, “because she’s doneexceptionally well.” I Apoorva Mandavilli is a freelance writerbased in New York. 1. Palmer, C. et al. PLoS Biol.   5, e177 (2007).2. Fishbein, T. et al. Gut   57, 323–330 (2008). See Editorial, page 563, and News Feature, page 578.     C    A    M    E    R    O    N    /    C    O    R    B    I    S An opportunity to track gut colonization. “We live for pooplike this.” —Stuart Kaufman 582 NATURE | Vol 453 | 29 May 2008 NEWS FEATURE HUMAN MICROBIOME