Human gut bacteria contain acquired interbacterial defence systems.

The human gastrointestinal tract consists of a dense and diverse microbial community, the composition of which is intimately linked to health. Extrinsic factors such as diet and host immunity are insufficient to explain the constituents of this community, and direct interactions between co-resident microorganisms have been implicated as important drivers of microbiome composition. The genomes of bacteria derived from the gut microbiome contain several pathways that mediate contact-dependent interbacterial antagonism1-3. Many members of the Gram-negative order Bacteroidales encode the type VI secretion system (T6SS), which facilitates the delivery of toxic effector proteins into adjacent cells4,5. Here we report the occurrence of acquired interbacterial defence (AID) gene clusters in Bacteroidales species that reside within the human gut microbiome. These clusters encode arrays of immunity genes that protect against T6SS-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements, and we show that their transfer is sufficient to confer resistance to toxins in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capability of a recombinase-associated AID subtype (rAID-1) that is present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins derived from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism by AID systems helps to shape human gut microbiome ecology.

seco-Pregnane Glycosides from Australian Caustic Vine (Cynanchum viminale subsp. australe).

Cynanchum viminale subsp. australe, more commonly known as caustic vine, is a leafless succulent that grows in the northern arid zone of Australia. Toxicity toward livestock has been reported for this species, along with use in traditional medicine and its potential anticancer activity. Disclosed herein are novel seco-pregnane aglycones cynavimigenin A (5) and cynaviminoside A (6), together with new pregnane glycosides cynaviminoside B (7) and cynavimigenin B (8). Cynavimigenin B (8) contains an unprecedented 7-oxobicyclo[2.2.1]heptane moiety in the seco-pregnane series, likely arising from a pinacol-type rearrangement. Interestingly, these isolates displayed only limited cytotoxicity in cancer and normal human cell lines, in addition to low activity against acetylcholinesterase and Sarcoptes scabiei bioassays, suggesting that 5-8 are not associated with the reported toxicity of this plant species.

Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies.

BACKGROUND: Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood. METHODS: We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of microbes and ARGs while adjusting for covariates. RESULTS: By 1 year, the abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95% CI: 0.19, 3.24) while Bacteroides fragilis decreased by 1.56% (95% CI: -4.32, 1.21). Bifidobacterium species also exhibited opposing trends. ARGs associated with exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use. CONCLUSION: Novel findings, including the importance of day care attendance, were identified through considering microbiome data at baseline and post-intervention. Thus, our study design and approach have important implications for future studies evaluating the unintended impacts of antibiotics. IMPACT: The impact of antibiotic exposure to off-target microbes and antibiotic resistance genes in the gut is poorly defined. We quantified these impacts in two cohort studies using a difference-in-differences approach. Novel to microbiome studies, we used pre/post-antibiotic data to emulate a randomized controlled trial. Compared to infants unexposed to antibiotics between baseline and 1 year, the relative abundance of multiple off-target species and antibiotic resistance genes was altered. Infants who attended day care and were exposed to antibiotics within the first year had a higher abundance of Escherichia coli and antibiotic resistance genes; a novel finding warranting further investigation.

The infant gut resistome is associated with E. coli and early-life exposures.

BACKGROUND: The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling were used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs. RESULTS: Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks' gestation) and 15 late preterm (33-36 weeks' gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux. The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically Escherichia coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs. Infants born via cesarean delivery had a trend towards a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97-1.29)] as well as having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12-1.84)] at 1 year compared to infants born vaginally. CONCLUSIONS: Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the risk of antibiotic resistant infections.

Oral Delivery of ß-Lactoglobulin-Nanosphere-Encapsulated Resveratrol Alleviates Inflammation in Winnie Mice with Spontaneous Ulcerative Colitis.

Resveratrol (RES) is a nutraceutical with promising anti-inflammatory properties for the treatment of inflammatory bowel diseases (IBD). However, the clinical effectiveness of resveratrol as an oral anti-inflammatory agent is hindered by its extremely poor solubility and poor stability. In this study, we encapsulated resveratrol in ß-lactoglobulin (BLG) nanospheres and systematically analyzed their formulation parameters in vitro followed by a thorough in vivo anti-inflammatory testing in a highly specialized spontaneous murine UC model (Winnie mice model). Complexation of resveratrol with BLG increased the aqueous solubility of resveratrol by ≈1.7 times with 10% w/w loading. Additionally, the in vitro dissolution of resveratrol from the particles was found to be higher compared to resveratrol alone, resulting in >90% resveratrol dissolution in ∼8 h. The anti-inflammatory activity of resveratrol was examined for the first time in Winnie mice, a mouse model that closely represents the clinical signs of IBD. At a 50 mg/kg oral dose for 2 weeks, BLG-RES significantly improved both % body weight and disease activity index (DAI), compared to free resveratrol in Winnie mice. Importantly, histological evaluations revealed a similar trend with striking improvement in the pathology of the colon via an increase in goblet cell numbers and recovery of colonic epithelium. BLG-RES significantly increased the expression level of cytokine interleukin-10 (Il10), which confirms the reduction in inflammation potentially because of the increased dissolution and stability of resveratrol by complexation with BLG. This comprehensive study demonstrates the effectiveness of biocompatible nanomaterials such as BLG in oral delivery of poorly soluble anti-inflammatory molecules such as resveratrol in the treatment of IBD.

Smad linker region phosphorylation is a signalling pathway in its own right and not only a modulator of canonical TGF-ß signalling.

Transforming growth factor (TGF)-ß signalling pathways are intensively investigated because of their diverse association with physiological and pathophysiological states. Smad transcription factors are the key mediators of TGF-ß signalling. Smads can be directly phosphorylated in the carboxy terminal by the TGF-ß receptor or in the linker region via multiple intermediate serine/threonine kinases. Growth factors in addition to hormones and TGF-ß can activate many of the same kinases which can phosphorylate the Smad linker region. Historically, Smad linker region phosphorylation was shown to prevent nuclear translocation of Smads and inhibit TGF-ß signalling pathways; however, it was subsequently shown that Smad linker region phosphorylation can be a driver of gene expression. This review will cover the signalling pathways of Smad linker region phosphorylation that drive the expression of genes involved in pathology and pathophysiology. The role of Smad signalling in cell biology is expanding rapidly beyond its role in TGF-ß signalling and many signalling paradigms need to be re-evaluated in terms of Smad involvement.

Effects of Antenatal Magnesium Sulfate on the Gut Function of Preterm (<32 weeks) Very Low Birth Weight Neonates: Experience from a Tertiary Institute in South India.

OBJECTIVE: Antenatal magnesium sulfate (MgSO4) is found to have various adverse effects in newborn, but the effect on preterm gut is still unclear. This study aimed to evaluate the effects of antenatal MgSO4 on preterm gut function by assessing the clinical outcomes and mesenteric blood flow. METHODS: This was a prospective cohort study on all preterm very low birth weight (VLBW) neonates born at a tertiary care center in South India from November 2016 to August 2017. Neonates with antenatal magnesium (Mg) exposure were compared with those with no exposure for various neonatal outcome variables like time to reach full feeds, feed intolerance, necrotizing enterocolitis (NEC) and other preterm complications, serial serum Mg levels and superior mesenteric artery (SMA) Doppler velocity measurements at two time points (24-48 h and 4-5 days after birth). RESULTS: Out of 84 neonates, 56 neonates were exposed to antenatal Mg with a median cumulative maternal dose of 28 g and the rest 28 neonates had no exposure. The mean time to reach full feeds was the same in both groups (10.5 days). Feed intolerance episodes were similar in the first week of life between the exposed and unexposed groups (48.2% vs. 46.4%; p = 0.88). Univariate analysis revealed no difference between groups concerning rates of NEC (p = 0.17) or mortality (p = 0.39). There was no significant difference in SMA Doppler parameters and hypermagnesemia between the two groups. CONCLUSION: Our study found no significant impact on postnatal feed tolerance and mesenteric blood flow among preterm VLBW neonates with antenatal MgSO4 exposure.

Foot Length for Gestational Age Assessment and Identification of High-Risk Infants: A Hospital-Based Cross-Sectional Study.

The knowledge of the gestational age of the newborn is essential for management. In the absence of a dating scan, the postnatal assessment scores have drawbacks of being difficult to learn and administer in the community. The measurement of the foot length is easy, reproducible and offers an objective assessment. The objective of this study was to determine the correlation of postnatal (<48 h) foot length measurement (with calipers) with gestational age as determined by antenatal dating ultrasound, create a predictive model for the same and propose foot length measurement cutoffs for <37 and <34 weeks of gestation. Secondary objectives were to assess the correlation between foot length as measured with calipers and that measured with a ruler and a paper footprint. This was a hospital-based cross-sectional study. Among the 520 babies assessed, the correlation of foot length with gestational age was 0.89. Operational cutoffs for the categories of <37 and <34 weeks at a sensitivity of 95% were <70 and <65 mm, respectively. The Pearson's correlation between foot length as measured by caliper and ruler was 0.95 and between caliper and paper footprint was 0.87. This study correlating foot length and gestational age has the potential to help neonatal care providers make informed management decisions, particularly in resource-limited settings.

Gender disparity in speakers at a major academic emergency medicine conference.

BACKGROUND: Although women make up a substantial portion of the workforce in emergency medicine, they remain under-represented in academia. METHODS: This study investigates trends in the representation of female speakers at the American College of Emergency Physicians scientific assembly-the largest academic emergency medicine conference in the world. Publication profiles, speaking duration and gender composition of speakers were collected and compared over a 3-year period. RESULTS: The authors described increased representation of female speakers at the conference from 2016 to 2018, as well as an upward trend in women's actual speaking time. CONCLUSION: This upward trend in women's representation may translate to more opportunities for female engagement in academic emergency medicine. Despite the increasing representation of women, male speakers outnumbered female speakers all 3 years, demonstrating that a speaker gender gap persists in academic emergency medicine.

Psychodynamic and sociopolitical predictors of COVID Distress and Gravity.

This study examined the relationship between attachment style and fear of contamination during the COVID-19 pandemic, hypothesizing that anxiously attached participants would be more distressed when their safe space was threatened by someone leaving and returning. During May 2020, n = 355 participants provided demographics, personality, health anxiety scores, attachment styles, political ideology, and attitudes towards the pandemic. In both social media and MTurk subsamples (but not in a subsample from a ListServ of professional psychologists), anxious attachment was a significant predictor of distress above and beyond personality and health anxiety. In addition, political ideology emerged as a consistent predictor of perceptions of the seriousness of COVID-19, even holding the other predictors constant. Understanding an individual's attachment style may be helpful in working with them in their trauma. This research also contributes to early empirical evidence for the impact of political ideology on self-reported attitudes and behaviors during the COVID-19 pandemic.

Rapid discovery of a selective butyrylcholinesterase inhibitor using structure-based virtual screening.

Acetylcholinesterase inhibitors are the mainstay of Alzheimer's disease treatments, despite having only short-term symptomatic benefits and severe side effects. Selective butyrylcholinesterase inhibitors (BuChEIs) may be more effective treatments in late-stage Alzheimer's disease with fewer side effects. Virtual screening is a powerful tool for identifying potential inhibitors in large digital compound databases. This study used structure-based virtual screening combined with physicochemical filtering to screen the InterBioScreen and Maybridge databases for novel selective BuChEIs. The workflow rapidly identified 22 potential hits in silico, resulting in the discovery of a human BuChEI with low-micromolar potency in vitro (IC50 2.4 µM) and high selectivity for butyrylcholinesterase over acetylcholinesterase. The compound was a rapidly reversible BuChEI with mixed-model in vitro inhibition kinetics. The binding interactions were investigated using in silico molecular dynamics and by developing structure-activity relationships using nine analogues. The compound also displayed high permeability in an in vitro model of the blood-brain barrier.

Transition to dental practice: Newly graduated dentists' views of being successful in dental practice.

BACKGROUND: The transition of dental graduates to the workforce is of interest to dental educators. The ways dentists think about success and successful practice tend to be tied to business parameters, patient flow and job satisfaction. These measures are narrow, however, and there is scant literature exploring success in ways that connects with professional identity formation. This study aims to add to scholarly understanding about the experiences of newly graduated dentists by asking: What is the variation in the ways new graduate dentists experience success in practice? METHODS: The qualitative methodology used in this study is phenomenography. Phenomenography studies the variation in the way a group of people experience a common phenomenon. In-depth, semi-structured interviews were conducted with 12 new dentists who had graduated from the University of Sydney. RESULTS: Five increasingly sophisticated, qualitatively distinct categories of description were identified: the day runs smoothly, keeping busy, providing quality patient care, generating personal meaning and having a sense of connection and belonging. CONCLUSIONS: This study gives insights into the complex ways newly graduated dentists think about successful dentistry. It broadens our view of successful practice beyond commercial aspects to include practitioner identity. Importantly, sense of responsibility, the practice environment and mentorship emerge as key players in this transitional career stage.

'Click' assembly of glycoclusters and discovery of a trehalose analogue that retards Aß40 aggregation and inhibits Aß40-induced neurotoxicity.

Osmolytes have been proposed as treatments for neurodegenerative proteinopathies including Alzheimer's disease. However, for osmolytes to reach the clinic their efficacy must be improved. In this work, copper(I)-catalyzed azide-alkyne cycloaddition chemistry was used to synthesize glycoclusters bearing six copies of trehalose, lactose, galactose or glucose, with the aim of improving the potency of these osmolytes via multivalency. A trehalose glycocluster was found to be superior to monomeric trehalose in its ability to retard the formation of amyloid-beta peptide 40 (Aß40) fibrils and protect neurons from Aß40-induced cell death.

Late-Preterm Antenatal Steroids for Reduction of Neonatal Respiratory Complications: A Randomized Controlled Trial.

OBJECTIVE: To evaluate the efficacy of antenatal corticosteroids in reducing neonatal respiratory complications when administered to those at risk of preterm delivery between 34 and 36 6/7 weeks of gestation. METHODS: This was a single-center, triple-blind, randomized, placebo-controlled trial in southern India enrolling pregnant participants at risk of preterm delivery between 34 and 36 6/7 weeks of gestation. Computer-generated block randomization was used with participants randomized to either one course of intramuscular betamethasone or placebo. The primary outcome was a composite of treatment for respiratory distress in the neonate, defined as need for oxygen or continuous positive airway pressure or mechanical ventilation for at least 2 hours in the first 72 hours of life. Neonatal secondary outcomes were transient tachypnea of the newborn, respiratory distress syndrome, necrotizing enterocolitis, sepsis, hyperbilirubinemia, hypoglycemia, stillbirth, and early neonatal death; maternal secondary outcomes were chorioamnionitis, postpartum hemorrhage, puerperal fever, and length of hospitalization. All analyses were based on intention to treat. A sample size of 1,200 was planned with 80% power to detect a 30% reduction in rates of respiratory distress. After a planned interim analysis, enrollment was stopped for futility. RESULTS: From March 2020 to August 2022, 847 participants were recruited, with 423 participants randomized to betamethasone and 424 participants randomized to placebo. There were 22 individuals lost to follow-up. There was no statistically significant difference in the primary outcome (betamethasone 4.9% vs placebo 4.8%, relative risk 1.03, 95% CI, 0.57-1.84, number needed to treat 786). There were no statistically significant differences in secondary neonatal or maternal outcomes. CONCLUSION: Betamethasone administered in the late-preterm period to those at risk for preterm delivery did not reduce the need for treatment of neonatal respiratory distress. CLINICAL TRIAL REGISTRATION: Clinical Trials Registry of India, CTRI/2019/09/021321.

Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota.

The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.

Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis.

Persons with cystic fibrosis (CF), starting in early life, show intestinal microbiome dysbiosis characterized in part by a decreased relative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid propionate. We demonstrate here that cystic fibrosis transmembrane conductance regulator-defective (CFTR-/-) Caco-2 intestinal epithelial cells are responsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1ß-induced inflammatory response of CFTR-/- Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. The introduction of Bacteroides-supplemented stool from infants with cystic fibrosis into the gut of CftrF508del mice results in higher propionate in the stool as well as the reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relative abundance of Escherichia coli, indicating a potential interaction between these two microbes, consistent with previous clinical studies. For a Bacteroides propionate mutant in the mouse model, pro-inflammatory cytokine KC is higher in the airway and serum compared with the wild-type (WT) strain, with no significant difference in the absolute abundance of these two strains. Taken together, our data indicate the potential multiple roles of Bacteroides-derived propionate in the modulation of systemic and airway inflammation and mediating the intestinal ecology of infants and children with CF. The roles of Bacteroides and the propionate it produces may help explain the observed gut-lung axis in CF and could guide the development of probiotics to mitigate systemic and airway inflammation for persons with CF.IMPORTANCEThe composition of the gut microbiome in persons with CF is correlated with lung health outcomes, a phenomenon referred to as the gut-lung axis. Here, we demonstrate that the intestinal microbe Bacteroides decreases inflammation through the production of the short-chain fatty acid propionate. Supplementing the levels of Bacteroides in an animal model of CF is associated with reduced systemic inflammation and reduction in the relative abundance of the opportunistically pathogenic group Escherichia/Shigella in the gut. Taken together, these data demonstrate a key role for Bacteroides and microbially produced propionate in modulating inflammation, gut microbial ecology, and the gut-lung axis in cystic fibrosis. These data support the role of Bacteroides as a potential probiotic in CF.

Cyclodextrin-crosslinked poly(acrylic acid): adhesion and controlled release of diflunisal and fluconazole from solid dosage forms.

The controlled release of diflunisal and fluconazole from tablets made of novel polymers, poly(acrylic acid) (PAA) crosslinked with either ß-cyclodextrin (ßCD) or hydroxypropyl-ßCD (HPßCD), was investigated and Carbopol 934P (Carbopol) was used as a highly crosslinked PAA for comparison. Diflunisal strongly associates with ßCD-PAA and HPßCD-PAA polymers (Ka of 486 and 6,055 M(-1) respectively); thus, it was physically mixed into the conjugates and also precomplexed to identify whether decomplexation has any influence on release kinetics. Fluconazole has poor complexing ability (Ka of 34 M(-1) with HPßCD-PAA); thus, it was only tested as a physical mixture. Swelling and adhesion studies were conducted on all tablet combinations and adhesivity of the CD-PAA polymer tablets was maintained. Diflunisal release was much slower from HPßCD-PAA tablets than from ßCD-PAA, suggesting that a higher degree of complexation retards release. The precomplexed diflunisal release was also slower than the physically mixed diflunisal of the corresponding conjugate. The release closely followed zero-order kinetics for HPßCD-PAA, but was more sigmoidal for ßCD-PAA and especially Carbopol. Conversely, poorly associating fluconazole released in almost exactly the same way across both polymers and Carbopol, indicating that the release kinetics of poorly associating drugs are not influenced by the presence of cyclodextrins. In view of the varying profiles and release rates shown with diflunisal for the different polymers, the fluconazole data support the concept that adequate complexation can indeed modulate the release kinetics of drugs.

Application of Nucleic Acid-Based Strategies to Detect Infectious Pathogens in Orthopaedic Implant-Related Infection.

➤: Implant-associated infection in orthopaedic surgery remains an enormous and largely unsolved clinical problem with a high rate of persistent or recurrent infection. This may be due, at least in part, to the potential for underdiagnosis by traditional microbial culture or the potential for culture to incompletely identify the microbial species present. ➤: Nucleic acid-based diagnostic techniques, focused on using the diagnostic information contained in DNA or RNA to identify microbial species, have been developing rapidly and have garnered escalating interest for both clinical and research applications. ➤: Commonly applied techniques include end-point polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and next-generation sequencing. Understanding the specific strengths and weaknesses of each technique is critical to understanding their utility, applying the correct assessment strategy, and critically understanding and interpreting research. ➤: The best practices for interpreting nucleic acid-based diagnostic techniques include considering positive and negative controls, reads per sample, detection thresholds (for differentiating contaminants from positive results), and the primer set or targeted regions.

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.

The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species whose prevalence and abundance reproducibly define microbiota development in early life in non-CF infants, but are missing or decreased in relative abundance in infants with CF. The consequences of these CF-specific differences in gut microbiota composition and dynamics are a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. We also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in CF, features that are associated with decreased gut bacterial density in inflammatory bowel diseases. Our results define key differences in the gut microbiota during ontogeny in CF and suggest the potential for directed therapies to overcome developmental delays in microbiota maturation.