The proportion of the human gut bacterial community that is recalcitrant to culture remains poorly defined. In this report, we combine high-throughput anaerobic culturing techniques with gnotobiotic animal husbandry and metagenomics to show that the human fecal microbiota consists largely of taxa and predicted functions that are represented in its readily cultured members. When transplanted into gnotobiotic mice, complete and cultured communities exhibit similar colonization dynamics, biogeographical distribution, and responses to dietary perturbations. Moreover, gnotobiotic mice can be used to shape these personalized culture collections to enrich for taxa suited to specific diets. We also demonstrate that thousands of isolates from a single donor can be clonally archived and taxonomically mapped in multiwell format to create personalized microbiota collections. Retrieving components of a microbiota that have coexisted in single donors who have physiologic or disease phenotypes of interest and reuniting them in various combinations in gnotobiotic mice should facilitate preclinical studies designed to determine the degree to which tractable bacterial taxa are able to transmit donor traits or influence host biology.gut bacterial diversity | nutrient-microbe interactions | translational medicine pipeline for human microbiome E fforts to dissect the functional interactions between microbial communities and their habitats are complicated by the longstanding observation that, for many of these communities, the great majority of organisms have not been cultured in the laboratory (1). Methodological differences between culture-independent and culture-based approaches have contributed to the challenge of deriving a realistic appreciation of exactly how much discrepancy exists between the culturable components of a microbial ecosystem and total community diversity. Table S1 gives examples of these methodological differences.The largest microbial community in the human body resides in the gut: Its microbiome contains at least two orders of magnitude more genes than are found in our Homo sapiens genome (2). Culture-independent metagenomic studies of the human gut microbiota are identifying microbial taxa and genes correlated with host phenotypes, but mechanistic and experimentally demonstrated links between key community members and specific aspects of host biology are difficult to establish with these methods alone. The goals of the present study were (i) to evaluate the representation of readily cultured phylotypes in the human gut microbiota; (ii) to profile the dynamics of these cultured communities in a mammalian gut ecosystem; and (iii) to determine whether a clonally arrayed, personalized strain collection could be constructed to serve as a foundation for reassembling varying elements of a human's gut microbiota in vitro or in vivo. ResultsTo estimate the abundance of readily cultured bacterial phylotypes in the distal human gut, primers were used to amplify variable region 2 (V2) of bacterial 16S ribosomal RNA (rRN...

Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.

Objective The study of posttraumatic growth (PTG) has burgeoned over the last decade, particularly in the area of oncology. The aims of the study were to: (1) describe PTG in patients with hepatobiliary carcinoma, (2) examine agreement between the patient and caregiver measures of patient PTG, and (3) test the associations between PTG and other better established psychological factors and clinically relevant outcomes. Methods Two hundred and two patients with hepatobiliary carcinoma completed a battery of standardized questionnaires that measured posttraumatic growth, depressive symptoms, optimism, expressed emotion, and quality of life. A subsample of family caregivers also completed ratings of patient PTG, using the Posttraumatic Growth Inventory (PTGI, as well as their own PTG. Results No significant increase in PTG was observed between diagnosis and 6-months follow-up with the exception of the Relating to Others subscale of the PTGI. PTG was not found to be associated with quality of life or depressive symptoms. At diagnosis, the agreement between the patients' PTG and family caregivers' rating of PTG was found to be high (ICC= 0.34-0.74, p=0.001-0.05). Posttraumatic growth was found to be significantly associated with optimism [r=0.20 p=0.02-.0.05] and traumatic life events reported in the past three years including recent losses [F(1,52)=6.0, p=0.02] and severe physical injury [F(1,52)=5.5, p=0.02]. Caregivers reported PTG as a result of their loved one's diagnosis of cancer. Conclusion Preliminary results suggest that PTG is relatively stable over the first 6-months after diagnosis and results in changes as a result of a diagnosis of cancer were reported, and possibly observed, by others. Family caregivers also experience PTG as a result of their loved one's diagnosis of advanced cancer.

BackgroundThe early life of the human host marks a critically important time for establishment of the gut microbial community, yet the developmental trajectory of gut community-encoded resistance genes (resistome) is unknown. We present a longitudinal study of the fecal antibiotic resistome of healthy amoxicillin-exposed and antibiotic-naive twins and their mothers during the first year of life.ResultsWe extracted metagenomic DNA (mgDNA) from fecal samples collected from three healthy twin pairs at three timepoints (1 or 2 months, 6 or 7 months, and 11 months) and from their mothers (collected at delivery). The mgDNA was used to construct metagenomic expression libraries in an Escherichia coli host. These libraries were screened for antibiotic resistance, and functionally selected resistance genes were sequenced and annotated. A diverse fecal resistome distinct from the maternal resistome was apparent by 2 months of age, and infants’ fecal resistomes included resistance to clinically important broad-spectrum beta-lactam antibiotics (e.g., piperacillin-tazobactam, aztreonam, cefepime) not found in their mothers. Dissemination of resistance genes among members of a given family was positively correlated with sharing of those same resistance genes between unrelated families, potentially identifying within-family sharing as a marker of resistance genes emerging in the human community at large. Finally, we found a distinct developmental trajectory for a community-encoded function: chloramphenicol resistance. All study subjects at all timepoints harbored chloramphenicol resistance determinants, but multidrug efflux pumps (rarely found in mothers) were the primary effectors of chloramphenicol resistance in young infants. Chloramphenicol acetyltransferases were more common in mothers than in infants and were found in nearly all the infants at later timepoints.ConclusionsOur results suggest that healthy 1–2-month-old infants’ gut microbes harbor clinically relevant resistance genes distinct from those of their mothers, and that family-specific shared environmental factors early in life shape resistome development.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-015-0090-9) contains supplementary material, which is available to authorized users.

Medical management of newborn infants often necessitates recurrent painful procedures, which may alter nociceptive pathways during a critical developmental period and adversely effect neuropsychological outcomes. To mitigate the effects of repeated painful stimuli, opioid administration for peri-procedural analgesia and ICU (intensive care unit) sedation is common in the NICU (neonatal intensive care unit). A growing body of basic and animal evidence suggests potential long-term harm associated with neonatal opioid therapy. Morphine increases apoptosis in human microglial cells, and animal studies demonstrate long-term changes in behavior, brain function, and spatial recognition memory following morphine exposure. This comprehensive review examines existing preclinical and clinical evidence on the long-term impacts of neonatal pain and opioid therapy.

The human intestinal microbiota encode multiple critical functions impacting human health, including metabolism of dietary substrate, prevention of pathogen invasion, immune system modulation, and provision of a reservoir of antibiotic resistance genes accessible to pathogens. The complexity of this microbial community, its recalcitrance to standard cultivation, and the immense diversity of its encoded genes has necessitated the development of novel molecular, microbiological, and genomic tools. Functional metagenomics is one such culture-independent technique, used for decades to study environmental microorganisms, but relatively recently applied to the study of the human commensal microbiota. Metagenomic functional screens characterize the functional capacity of a microbial community, independent of identity to known genes, by subjecting the metagenome to functional assays in a genetically tractable host. Here we highlight recent work applying this technique to study the functional diversity of the intestinal microbiota, and discuss how an approach combining high-throughput sequencing, cultivation, and metagenomic functional screens can improve our understanding of interactions between this complex community and its human host.

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