Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers.

OBJECTIVES: The relevance of spatial composition in the microbial changes associated with UC is unclear. We coupled luminal brush samples, mucosal biopsies and laser capture microdissection with deep sequencing of the gut microbiota to develop an integrated spatial assessment of the microbial community in controls and UC. DESIGN: A total of 98 samples were sequenced to a mean depth of 31,642 reads from nine individuals, four control volunteers undergoing routine colonoscopy and five patients undergoing surgical colectomy for medically-refractory UC. Samples were retrieved at four colorectal locations, incorporating the luminal microbiota, mucus gel layer and whole mucosal biopsies. RESULTS: Interpersonal variability accounted for approximately half of the total variance. Surprisingly, within individuals, asymmetric Eigenvector map analysis demonstrated differentiation between the luminal and mucus gel microbiota, in both controls and UC, with no differentiation between colorectal regions. At a taxonomic level, differentiation was evident between both cohorts, as well as between the luminal and mucosal compartments, with a small group of taxa uniquely discriminating the luminal and mucosal microbiota in colitis. There was no correlation between regional inflammation and a breakdown in this spatial differentiation or bacterial diversity. CONCLUSIONS: Our study demonstrates a conserved spatial structure to the colonic microbiota, differentiating the luminal and mucosal communities, within the context of marked interpersonal variability. While elements of this structure overlap between UC and control volunteers, there are differences between the two groups, both in terms of the overall taxonomic composition and how spatial structure is ascribable to distinct taxa.

Correlations between colonic crypt mucin chemotype, inflammatory grade and Desulfovibrio species in ulcerative colitis.

AIM: The colonic mucus gel layer is composed of mucins that may be sulphated or sialyated. Sulphated mucins predominate in health while in ulcerative colitis (UC) sulphation is reduced. These differences result directly from inflammatory events. It may also be hypothesized that they arise in part from alterations in the colonic microbiota, particularly changes in the burden of sulphated mucin-metabolizing species, such as Desulfovibrio (DSV) bacteria. The aim of this study was to correlate colonic mucin chemotypes and inflammatory scores in health and UC and relate these changes to changes in the colonization of colonic crypts by DSV. METHOD: Paired colonic biopsies from 34 healthy controls (HC) and 19 patients with active UC were collected for the purpose of parallel histological and microbiological assessment. High-iron diamine and Alcian blue staining and haematoxylin and eosin of mucosal biopsy specimens were used to assess histological changes within the clinical spectrum of UC. Quantitative real-time polymerase chain reaction analysis was employed to determine the total and DSV copy number within the colonic crypts. RESULTS: Compared with HC, the mucin chemotype in UC was less sulphated and inversely correlated with the degree of mucosal inflammation. A weak but significant negative correlation was found between the abundance of sulphated mucins and DSV burden. CONCLUSION: Mucin composition strongly correlates with the degree of mucosal inflammation, and to a lesser extent with DSV burden. These data suggest that mucin chemotype and DSV burden are linked phenomena and highlight the need to consider changes in mucin chemotype in the setting of microbial dysbiosis occurring within the colitic colon. What does this paper add to the literature? Decreased sulphation of mucins has been associated with inflammation in ulcerative colitis. Currently there are few data describing the relationship between microbial species and changes in mucin chemotype. This study validates previous findings and presents evidence of changes in mucin chemotype occurring in tandem with coherent changes in the microbiota within crypt niches.

Comparison of fidaxomicin, thuricin CD, vancomycin and nisin highlights the narrow spectrum nature of thuricin CD.

Vancomycin and metronidazole are commonly used treatments for Clostridioides difficile infection (CDI). However, these antibiotics have been associated with high levels of relapse in patients. Fidaxomicin is a new treatment for CDI that is described as a narrow spectrum antibiotic that is minimally active on the commensal bacteria of the gut microbiome. The aim of this study was to compare the effect of fidaxomicin on the human gut microbiome with a number of narrow (thuricin CD) and broad spectrum (vancomycin and nisin) antimicrobials. The spectrum of activity of each antimicrobial was tested against 47 bacterial strains by well-diffusion assay. Minimum inhibitory concentrations (MICs) were calculated against a select number of these strains. Further, a pooled fecal slurry of 6 donors was prepared and incubated for 24 h with 100 µM of each antimicrobial in a mini-fermentation system together with a no-treatment control. Fidaxomicin, vancomycin, and nisin were active against most gram positive bacteria tested in vitro, although fidaxomicin and vancomycin produced larger zones of inhibition compared to nisin. In contrast, the antimicrobial activity of thuricin CD was specific to C. difficile and some Bacillus spp. The MICs showed similar results. Thuricin CD exhibited low MICs (<3.1 µg/mL) for C. difficile and Bacillus firmus, whereas fidaxomicin, vancomycin, and nisin demonstrated lower MICs for all other strains tested when compared to thuricin CD. The narrow spectrum of thuricin CD was also observed in the gut model system. We conclude that the spectrum of activity of fidaxomicin is comparable to that of the broad-spectrum antibiotic vancomycin in vitro and the broad spectrum bacteriocin nisin in a complex community.

Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9-/- mice to colitis.

BACKGROUND: The etiology of inflammatory bowel disease (IBD) is unclear but involves both genetics and environmental factors, including the gut microbiota. Indeed, exacerbated activation of the gastrointestinal immune system toward the gut microbiota occurs in genetically susceptible hosts and under the influence of the environment. For instance, a majority of IBD susceptibility loci lie within genes involved in immune responses, such as caspase recruitment domain member 9 (Card9). However, the relative impacts of genotype versus microbiota on colitis susceptibility in the context of CARD9 deficiency remain unknown. RESULTS: Card9 gene directly contributes to recovery from dextran sodium sulfate (DSS)-induced colitis by inducing the colonic expression of the cytokine IL-22 and the antimicrobial peptides Reg3ß and Reg3γ independently of the microbiota. On the other hand, Card9 is required for regulating the microbiota capacity to produce AhR ligands, which leads to the production of IL-22 in the colon, promoting recovery after colitis. In addition, cross-fostering experiments showed that 5 weeks after weaning, the microbiota transmitted from the nursing mother before weaning had a stronger impact on the tryptophan metabolism of the pups than the pups' own genotype. CONCLUSIONS: These results show the role of CARD9 and its effector IL-22 in mediating recovery from DSS-induced colitis in both microbiota-independent and microbiota-dependent manners. Card9 genotype modulates the microbiota metabolic capacity to produce AhR ligands, but this effect can be overridden by the implantation of a WT or "healthy" microbiota before weaning. It highlights the importance of the weaning reaction occurring between the immune system and microbiota for host metabolism and immune functions throughout life. A better understanding of the impact of genetics on microbiota metabolism is key to developing efficient therapeutic strategies for patients suffering from complex inflammatory disorders. Video Abstract.

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts.

We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample ß-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.

Accuracy of cricothyroid membrane identification using ultrasound and palpation techniques in obese obstetric patients: an observational study.

BACKGROUND: During performance of emergency front of neck access, the final step in management algorithms for the 'can't intubate, can't oxygenate' scenario, accurate identification of the cricothyroid membrane is crucial. Accurate identification using palpation techniques is low, with highest failure rates occurring in obese females. METHODS: This prospective observational study recruited 28 obese obstetric patients. The cricothyroid membrane was identified using ultrasound, marked with an ultraviolet pen and covered with a dressing. The candidate was asked to perform cricothyroid membrane identification using landmark technique (group L) followed by ultrasound (group U). The primary outcome was the distance between the actual and estimated cricothyroid membrane midpoint. Secondary outcomes were the proportion of accurate assessments, time taken, and subjective ease of identification using a visual analogue score. RESULTS: Distance from the cricothyroid membrane midpoint was shorter in group U than Group L (2.5 mm vs 5.5 mm, P=0.002). The proportion of correctly identified cricothyroid membranes was greater in group U than group L (71% vs 39%, P=0.015). Time required for identification was shorter in group L than group U (16.9 s vs 23.5 s, P=0.001). Visual analogue scores for ease of identification were lower in group U than group L (2.4 cm vs 4.2 cm, P=0.013). CONCLUSIONS: Ultrasound-guided cricothyroid membrane localisation was significantly more accurate but slower than the landmark technique in obese obstetric patients. As such, we recommend the use of pre-procedural identification of the cricothyroid membrane in this patient population and formal training of anaesthetists in airway ultrasound.

Morphometry of nuclei, nuclear envelopes and nucleoli in aging hamster cerebrum.

The neuronal nucleus and nucleolus undergo extensive dimensional and configurational changes during maturation and aging, as shown in this study of pyramidal cells of the hamster motor cortex. With maturation, the increase in nuclear perimeter length per unit nuclear area was associated with an increased amount of nuclear invaginations. With maturation and aging, there was a change in nuclear caliper shape, from spherical to very nonspherical. The number of nucleoli containing microbodies peaked first at 15 days and again at 600 days. It is concluded that area, perimeter and form factor relate to nuclear caliper shape and the presence of nucleolar microbodies. The correlated changes in these parameters appear to differentially reflect stage-specific metabolic conditions related to two critical phases: (1) an early phase (10-15 days) at the inception of configurational changes leading to maturity, and (2) a late phase (600-700 days) at the inception of configurational changes leading to old age.

Nuclear envelope invaginations in hamster pyramidal cells during development and aging.

Nuclear envelope invaginations were observed in pyramidal cell nuclei of the hamster frontal cortex during development and aging. These invaginations which began to appear at 10 day did not recede at maturity as has been observed in certain other cell types, but persisted in the adult hamster and during subsequent aging. Morphometric data showed a significant increase in the number of nuclear envelope invaginations and in their length per unit of the nucleus. This increase was positively correlated with age until 500 days and is suggestive of a continued high metabolic activity that did not subside following the rapid growth phase of the pyramidal neurons.

Ultrastructural and morphometric analysis of nucleolar and nuclear changes during the early growth period in hamster facial neurons.

In this study, progressive developmental changes in the nucleus and associated organelles, including the nucleolus, coiled bodies, nuclear envelope, and nucleoplasm, of hamster facial motor neurons were characterized by two parallel analyses: ultrastructural and morphometric. Golden hamsters (Mesocricetus auratus) used for this series were the 14-day fetus, newborn (less than 6 hr), and 1, 2, 3, 4, 5, 7, 9, 11 and 13 days postnatal ages, with 3 animals per group. Following anesthesia and perfusion fixation, facial nuclear groups were dissected and processed for electron microscopy. Electron micrographs and camera lucida tracings of nuclear profiles were collected and analyzed. The ultrastructural analysis revealed progressive changes in the nucleolus from a compact, segregated type to a reticulated form characteristic of actively protein-secreting cells. Nucleolar microbodies and fibrillar centers were seen at all ages; the latter structures appeared to decrease in size and increase with age in the series. The nucleolus-associated chromatin became less condensed, suggesting an increase in the incorporation of rDNA into the nucleolus proper. Coiled bodies, both free and attached to nucleoli, were found in varying frequencies. The nucleoplasm of neurons at the earliest stages contained large numbers of heterochromatin clumps, which decreased concomitantly with an increase in interchromatin granules and fibrils during the later stages. Nuclear envelope invaginations, polarized along one side of the nucleus, increased throughout the developmental period examined. These changes occurred in concert with a 61% increase in nuclear size and a 47% increase in the length of nuclear envelope. The sequence of nuclear changes observed during this early period of normal facial neuronal growth completes the study of a series of distinctly defined cytomorphic events in this cell type, the lability of which can be experimentally tested for their functional roles in neuronal development.

Ultrastructural changes in the nucleolus of facial motor neurons following axotomy during an early critical period in development.

In this study, the effects of axotomy on the ultrastructure of the nucleolus and associated organelles were examined in fetal, newborn, and early postnatal facial motoneurons of the hamster. Golden hamsters used for this study were the 14-day fetus, newborn (0 days; less than 6 hr) and 2, 4, 7, and 9 days postnatal ages, with 3 animals per group. For prenatal surgeries, pregnant hamsters were anesthetized and the facial nerves severed in the fetuses via electrocautery through the uterine wall and amniotic membrane. For postnatal surgeries, the animals were anesthetized and the right facial nerve exposed and severed at its exit from the stylomastoid foramen. At the appropriate postoperative times, the animals were reanesthetized and perfused-fixed. The facial nuclear groups were dissected and processed for routine electron microscopy. Microbody and coiled body frequencies were determined from the number of neurons containing these structures per number of neurons sampled per animal in each experimental or control group and subjected to statistical analysis. Nucleolar reactive changes that occurred during this developmental sequence fell into two major categories. The first category displayed by most injured cells consisted of an initial compacting of fibrillar material and reduction in vacuolar space. The second category appeared to represent a progression from this first stage of nucleolar reactivity into degenerative changes involving a striking segregation of nucleolar components into five distinct regions. The incidence of microbodies increased as a result of axotomy, whereas the presence of coiled bodies decreased at the later postoperative stages in the older animals. With increasing age and nucleolar maturation, the nucleolar reactive pattern became less pronounced and severe, and neuronal survival predominated. It appears, therefore, that the two categories of nucleolar changes following axotomy during early development correlate with changes observed in nucleoli under conditions of rRNA downregulation. It is hypothesized from these results that a key step in the ability of neurons to survive axotomy and successfully regenerate at these early developmental stages occurs at some point in ribosomal RNA transcription and/or processing. Complementary information at the molecular level concerning changes in nucleolar synthetic activity and ribosome production will be necessary to test this hypothesis.

Morphological changes of the pyramidal cell nucleolus and nucleus in hamster frontal cortex during development and aging.

The development and aging of the nucleolus and nucleus in layer V pyramidal cells in the hamster cerebrum were studied by light and electron microscopy. The nucleoli appeared in the newborn as occasional fibrillar masses adjacent to peripherally placed bodies of chromatin. By maturity, a single, generally central, nucleolus proper with nucleolus-associated chromatin was present. Nucleolar microbodies were observed at 10, 15, 20 and 480 days, but not in the newborn, 5-or 90-day animal. An intranucleolar body was not observed at the electron at the electron-microscopy level in these pyramidal cell nucleoli at any age in this series, in contrast to the situation in large motor neurons of the facial nucleus. The nucleus progressed from an irregular shape at birth to an oval shape at maturity. At 10 days, incipient invaginations of the nuclear membrane appeared; these subsequently increased in depth and frequency in the adult. The above changes, particularly in the nucleoli, are correlated in time with changes involving the endoplasmic reticulum. The correlations may indicate different periods of metabolic activity in the hamster pyramidal neurons. Four such periods can be differentiated on the basis of cytomorphic changes which may be correlated to reported development of function. The sequence of these changes, peculiar to the developing and aging hamster pyramidal neuron, differs from that seen in large spinal and cranial motor neurons. It appears that some features of nuclear immaturity, which are lost in larger neuronal types, are retained in the adult pyramidal neuron.

Investigation of the prejunctional alpha2-adrenoceptor mediated actions of MDMA in rat atrium and vas deferens.

1. We have investigated the effects of methylenedioxymethamphetamine (MDMA, 'ecstasy') on peripheral noradrenergic neurotransmission in the rat. 2. In rat atrial slices pre-incubated with [3H]-noradrenaline and in the presence of desipramine (1 micronM) to prevent effects of MDMA on basal outflow of tritium, MDMA (10 micronM) significantly inhibited the release of tritium evoked by short trains of six pulses at 100 Hz every 10 s for 3 min. This effect did not occur in the presence of the alpha2-adrenoceptor antagonist yohimbine (1 micronM). 3. In epididymal portions of rat vas deferens in the presence of nifedipine (10 micronM), MDMA produced a concentration-dependent inhibition of single pulse nerve stimulation-evoked contractions with a pD2 of 5.88+/-0.16 (n=4). Inhibitory effects of MDMA were antagonized by the alpha2-adrenoceptor antagonist yohimbine (0.3 micronM), but not by the 5-hydroxytryptamine receptor antagonist cyanopindolol in a concentration (1 micronM) which markedly antagonized the inhibitory actions of the 5-HT-1 receptor agonist 5-carboxamidotryptamine. 4. In prostatic portions of rat vas deferens in the presence of cocaine (3 micronM), MDMA produced a concentration-dependent inhibition of single pulse nerve stimulation-evoked contractions with a pD2 of 5. 12+/-0.21 (n=4). In the absence of cocaine, only the highest concentration of MDMA (30 micronM) produced an inhibition, but the alpha2-adrenoceptor antagonist yohimbine (0.3 micronM) converted the response to MDMA from inhibition to potentiation of the stimulation-evoked contraction. 5. In radioligand binding studies, MDMA showed similar affinities for alpha2B, alpha2C and alpha2D-adrenoceptor sites, with pKi values of 5.14+/-0.16, 5.11+/-0. 05 and 5.31+/-0.14, respectively. 6 It is concluded that MDMA has significant alpha2-adrenoceptor agonist actions.