Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth

The gut microbiota (GM) is essential for mammalian health. Although the association between infant GM and breast milk (BM) composition has been well established in humans, such a relationship has not been investigated in horses. Hence, this study was conducted to analyze the GM formation of foals during lactation and determine the presence of low-molecular-weight metabolites in mares' BM and their role in shaping foals' GM. The fecal and BM samples from six pairs of foals and mares were subjected to 16S ribosomal RNA metagenomic and metabolomic analyses, respectively. The composition of foal GM changed during lactation time; hierarchical cluster analysis divided the fetal GM into three groups corresponding to different time points in foal development. The level of most metabolites in milk decreased over time with increasing milk yield, while threonic acid and ascorbic acid increased. Further analyses revealed gut bacteria that correlated with changes in milk metabolites; for instance, there was a positive correlation between Bacteroidaceae in the foal's gut microbiota and serine/glycine in the mother's milk. These findings help improve the rearing environment of lactating horses and establish artificial feeding methods for foals.

Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly

Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.

Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants

Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.

Intra-hospital microbiome variability is driven by accessibility and clinical activities

The hospital environmental microbiome, which can affect patients' and healthcare workers' health, is highly variable and the drivers of this variability are not well understood. In this study, we collected 37 surface samples from the neonatal intensive care unit (NICU) in an inpatient hospital before and after the operation began. Additionally, healthcare workers collected 160 surface samples from five additional areas of the hospital. All samples were analyzed using 16S rRNA gene amplicon sequencing, and the samples collected by healthcare workers were cultured. The NICU samples exhibited similar alpha and beta diversities before and after opening, which indicated that the microbiome there was stable over time. Conversely, the diversities of samples taken after opening varied widely by area. Principal coordinate analysis (PCoA) showed the samples clustered into two distinct groups: high alpha diversity [the pediatric intensive care unit (PICU), pathology lab, and microbiology lab] and low alpha diversity [the NICU, pediatric surgery ward, and infection prevention and control (IPAC) office]. Least absolute shrinkage and selection operator (LASSO) classification models identified 156 informative amplicon sequence variants (ASVs) for predicting the sample's area of origin. The testing accuracy ranged from 86.37% to 100%, which outperformed linear and radial support vector machine (SVM) and random forest models. ASVs of genera that contain emerging pathogens were identified in these models. Culture experiments had identified viable species among the samples, including potential antibiotic-resistant bacteria. Though area type differences were not noted in the culture data, the prevalences and relative abundances of genera detected positively correlated with 16S sequencing data. This study brings to light the microbial community temporal and spatial variation within the hospital and the importance of pathogenic and commensal bacteria to understanding dispersal patterns for infection control.

IMPORTANCE

We sampled surface samples from a newly built inpatient hospital in multiple areas, including areas accessed by only healthcare workers. Our analysis of the neonatal intensive care unit (NICU) showed that the microbiome was stable before and after the operation began, possibly due to access restrictions. Of the high-touch samples taken after opening, areas with high diversity had more potential external seeds (long-term patients and clinical samples), and areas with low diversity and had fewer (short-term or newborn patients). Classification models performed at high accuracy and identified biomarkers that could be used for more targeted surveillance and infection control. Though culturing data yielded viability and antibiotic-resistance information, it disproportionately detected the presence of genera relative to 16S data. This difference reinforces the utility of 16S sequencing in profiling hospital microbiomes. By examining the microbiome over time and in multiple areas, we identified potential drivers of the microbial variation within a hospital.

Social and environmental predictors of gut microbiome age in wild baboons

Understanding why some individuals age faster than others is essential to evolutionary biology and geroscience, but measuring variation in biological age is difficult. One solution may lie in measuring gut microbiome composition because microbiota change with many age-related factors (e.g., immunity and behavior). Here we create a microbiome-based age predictor using 13,563 gut microbial profiles from 479 wild baboons collected over 14 years. The resulting "microbiome clock" predicts host chronological age. Deviations from the clock's predictions are linked to demographic and socio-environmental factors that predict baboon health and survival: animals who appear old-for-age tend to be male, sampled in the dry season (for females), and high social status (both sexes). However, an individual's "microbiome age" does not predict the attainment of developmental milestones or lifespan. Hence, the microbiome clock accurately reflects age and some social and environmental conditions, but not the pace of development or mortality risk.

Towards more accurate microbial source tracking via non-negative matrix factorization (NMF)

MOTIVATION

The microbiome of a sampled habitat often consists of microbial communities from various sources, including potential contaminants. Microbial source tracking (MST) can be used to discern the contribution of each source to the observed microbiome data, thus enabling the identification and tracking of microbial communities within a sample. Therefore, MST has various applications, from monitoring microbial contamination in clinical labs to tracing the source of pollution in environmental samples. Despite promising results in MST development, there is still room for improvement, particularly for applications where precise quantification of each source's contribution is critical.

RESULTS

In this study, we introduce a novel tool called SourceID-NMF towards more precise microbial source tracking. SourceID-NMF utilizes a non-negative matrix factorization (NMF) algorithm to trace the microbial sources contributing to a target sample. By leveraging the taxa abundance in both available sources and the target sample, SourceID-NMF estimates the proportion of available sources present in the target sample. To evaluate the performance of SourceID-NMF, we conducted a series of benchmarking experiments using simulated and real data. The simulated experiments mimic realistic yet challenging scenarios for identifying highly similar sources, irrelevant sources, unknown sources, low abundance sources, and noise sources. The results demonstrate the superior accuracy of SourceID-NMF over existing methods. Particularly, SourceID-NMF accurately estimated the proportion of irrelevant and unknown sources while other tools either over- or under-estimated them. In addition, the noise sources experiment also demonstrated the robustness of SourceID-NMF for MST.

AVAILABILITY AND IMPLEMENTATION

SourceID-NMF is available online at https://github.com/ZiyiHuang0708/SourceID-NMF.

Difference in the Intestinal Microbiota between Breastfeed Infants and Infants Fed with Artificial Milk: A Systematic Review

The gut microbiota (GM) plays a crucial role in human health, particularly during the first years of life. Differences in GM between breastfed and formula (F)-fed infants may influence long-term health outcomes. This systematic review aims to compare the gut microbiota of breastfed infants with that of F-fed infants and to evaluate the clinical implications of these differences. We searched databases on Scopus, Web of Science, and Pubmed with the following keywords: "gut microbiota", "gut microbiome", and "neonatal milk". The inclusion criteria were articles relating to the analysis of the intestinal microbiome of newborns in relation to the type of nutrition, clinical studies or case series, excluding reviews, meta-analyses, animal models, and in vitro studies. The screening phase ended with the selection of 13 publications for this work. Breastfed infants showed higher levels of beneficial bacteria such as Bifidobacterium and Lactobacillus, while F-fed infants had a higher prevalence of potentially pathogenic bacteria, including Clostridium difficile and Enterobacteriaceae. Infant feeding type influences the composition of oral GM significantly. Breastfeeding promotes a healthier and more diverse microbial ecosystem, which may offer protective health benefits. Future research should explore strategies to improve the GM of F-fed infants and understand the long-term health implications.

Linking preterm infant gut microbiota to nasograstric enteral feeding tubes: exploring potential interactions and microbial strain transmission

Introduction

Preterm birth is a growing problem worldwide. Staying at a neonatal intensive care unit (NICU) after birth is critical for the survival of preterm infants whose feeding often requires the use of nasogastric enteral feeding tubes (NEFT). These can be colonized by hospital-associated pathobionts that can access the gut of the preterm infants through this route. Since the gut microbiota is the most impactful factor on maturation of the immune system, any disturbance in this may condition their health. Therefore, the aim of this study is to assess the impact of NEFT-associated microbial communities on the establishment of the gut microbiota in preterm infants.

Material and methods

A metataxonomic analysis of fecal and NEFT-related samples obtained during the first 2 weeks of life of preterm infants was performed. The potential sharing of strains isolated from the same set of samples of bacterial species involved in NICU's outbreaks, was assessed by Random Amplification of Polymorphic DNA (RAPD) genotyping.

Results

In the samples taken 48 h after birth (NEFT-1 and Me/F1), Staphylococcus spp. was the most abundant genera (62% and 14%, respectively) and it was latter displaced to 5.5% and 0.45%, respectively by Enterobacteriaceae. Significant differences in beta diversity were detected in NEFT and fecal samples taken at day 17 after birth (NEFT-3 and F3) (p = 0.003 and p = 0.024, respectively). Significant positive correlations were found between the most relevant genera detected in NEFT-3 and F3. 28% of the patients shared at least one RAPD-PCR profile in fecal and NEFT samples and 11% of the total profiles were found at least once simultaneously in NEFT and fecal samples from the same patient.

Conclusion

The results indicate a parallel bacterial colonization of the gut of preterm neonates and the NEFTs used for feeding, potentially involving strain sharing between these niches. Moreover, the same bacterial RAPD profiles were found in neonates hospitalized in different boxes, suggesting a microbial transference within the NICU environment. This study may assist clinical staff in implementing best practices to mitigate the spread of pathogens that could threaten the health of preterm infants.

Trends in viable microbial bioburden on surfaces within a paediatric bone marrow transplant unit

BACKGROUND

Despite their role being historically overlooked, environmental surfaces have been shown to play a key role in the transmission of pathogens causative of healthcare-associated infection. To guide infection prevention and control (IPC) interventions and inform clinical risk assessments, more needs to be known about microbial surface bioburdens.

AIM

To identify the trends in culturable bacterial contamination across communal touch sites over time in a hospital setting.

METHODS

Swab samples were collected over nine weeks from 22 communal touch sites in a paediatric bone marrow transplant unit. Samples were cultured on Columbia blood agar and aerobic colony counts (ACC) per 100 cm2 were established for each site. Individual colony morphologies were grouped and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or 16s rDNA sequencing.

FINDINGS

Highest mean counts were observed for sites associated with ward management activity and computer devices (3.29 and 2.97 ACC/100 cm2 respectively). A nurses' station keyboard had high mean ACC/100 cm2 counts (10.67) and diversity, while laundry controls had high mean ACC/100 cm2 counts (4.70) and low diversity. Micrococcus luteus was identified in all sampling groups. Clinical staff usage sites were contaminated with similar proportions of skin and environmental flora (52.19-46.59% respectively), but sites associated with parental activities were predominantly contaminated by environmental microflora (86.53%).

CONCLUSION

The trends observed suggest patterns in microbial loading based on site activities, surface types and user groups. Improved understanding of environmental surface contamination could help support results interpretation and IPC interventions, improving patient safety.

Influence of infant microbiome on health and development

The microbiome is a complex ecosystem comprising microbes, their genomes, and the surrounding environment. The microbiome plays a critical role in early human development, including maturation of the host immune system and gastrointestinal tract. Multiple factors, including diet, anti-biotic use, and other environmental exposures, influence the establishment of the microbiome during infancy. Numerous studies have identified associations between the microbiome and neonatal diseases, including necrotizing enterocolitis, sepsis, and malnutrition. Furthermore, there is compelling evidence that perturbation of the microbiome in early life can have lasting developmental effects that increase an individual's risk for immune and metabolic diseases in later life. Supplementation of the microbiome with probiotics reduces the risk of necrotizing enterocolitis and sepsis in at-risk infants. This review focuses on the structure and function of the infant microbiome, the environmental and clinical factors that influence its assembly, and its impact on infant health and development.

Sociodemographic Factors and Intestinal Microbiome Development in Preterm, Very Low Birth Weight Infants

OBJECTIVE

Preterm very low birth weight (VLBW) infants are at risk for intestinal morbidities and dysbiotic development of the intestinal microbiome. Despite the influence of sociodemographic factors on premature infant health outcomes, whether they shape the intestinal microbiome early in life is not clear. The objective was to explore the associations between race, sex, and socioeconomic status and the intestinal microbiome of VLBW infants during the first 4 weeks of life.

STUDY DESIGN

This was a secondary analysis of data from an ongoing randomized trial of 79 infants ≤30 weeks' gestation and ≤1,500 g. Stool samples were collected at week 1 through week 4, frozen to -80°C and analyzed by 16S rRNA sequencing of the V4 region using Illumina MiSeq. Reads were analyzed to measure α and β diversity as well as relative abundance of bacteria in the intestinal microbiome.

RESULTS

Of the 79 infants, 63 had at least one sample available. Twenty-three (37%) of infants were African American, 30 (48%) were male, and 44 (71%) had Medicaid insurance. There were no statistically significant (<0.05) differences in α diversity or β diversity, and the differential abundance analysis suggests limited patterns of distinction in the intestinal microbiome between non-African American and African American infants, male and female infants, and infants with maternal private or Medicaid insurance.

CONCLUSION

Our results suggest race, sex, and socioeconomic status shape colonization of specific microorganisms to a limited extent. Future studies should confirm these findings and determine clinical relevance through further study of differentially abundant microorganisms and additional factors contributing to colonization patterns.

KEY POINTS

· Diversity of the gut microbiome was similar between infants of varying race, sex, and socioeconomic status.. · We observed sociodemographic-linked differences in colonization of individual taxa.. · Further study is required to confirm these results and the clinical relevance of these findings..

Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis

Though statistical normalizations are often used in differential abundance or differential expression analysis to address sample-to-sample variation in sequencing depth, we offer a better alternative. These normalizations often make strong, implicit assumptions about the scale of biological systems (e.g., microbial load). Thus, analyses are susceptible to even slight errors in these assumptions, leading to elevated rates of false positives and false negatives. We introduce scale models as a generalization of normalizations so researchers can model potential errors in assumptions about scale. By incorporating scale models into the popular ALDEx2 software, we enhance the reproducibility of analyses while often drastically decreasing false positive and false negative rates. We design scale models that are guaranteed to reduce false positives compared to equivalent normalizations. At least in the context of ALDEx2, we recommend using scale models over normalizations in all practical situations.

Influence of connatural factors in shaping vaginal microflora and ensuring its health

Vaginal canal (VC) is exposed to the external environment affected by habitual factors like hygiene and sexual behaviour as well as physiological factors like puberty, menstrual cycle, pregnancy, child birth and menopause. Healthy VC harbours beneficial microflora supported by vaginal epithelium and cervical fluid. Connatural antimicrobial peptide (AMPs) of female reproductive tract (FRT) conjunctly with these beneficial microbes provide protection from a large number of infectious diseases. Such infections may either be caused by native microbes of the VC or transitory microbes like bacteria or virus which are not a part of VC microflora. This review highlight's the role of hormones, enzymes, innate immunological factors, epithelial cells and vaginal mucus that support beneficial microbes over infectious ones thus, helping to maintain homeostasis in VC and further protect the FRT. We also discuss the prospective use of vaginal probiotics and AMPs against pathogens which can serve as a potential cure for vaginal infections.

Gut microbiota of preterm infants in the neonatal intensive care unit: a study from a tertiary care center in northern India

Introduction

Disruptions of the gut microbiota of preterm infants admitted to the neonatal intensive care unit (NICU) during the first 2 weeks of life are of critical importance. These infants are prone to various complications, including necrotizing enterocolitis (NEC) and sepsis. Studying the gut microbiota will improve outcomes in preterm infants. In the present study, we examined the gut microbiota of preterm infants admitted to the NICU in the first month of life.

Methods

Neonates admitted to the NICU were recruited, and stool samples were collected weekly from the seventh day of the infant's life until the 30th day of life. DNA was extracted using a DNeasy Powersoil DNA isolation kit. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the MiSeq platform. Sequenced reads were processed on DADA2 pipeline to obtain an amplicon sequence variant (ASV) table. All bioinformatic and statistical analyses were performed using different packages in the R statistical framework.

Results

Fourteen preterm infants were recruited, and 48 samples were collected. Alpha diversity metrics, observed ASV count, and Shannon index were found to have no differences in any clinical variables. Permutational multivariate analysis of variance (PERMANOVA) showed discrimination of neonates by gestational age and administration of probiotics. Differential abundance analysis showed a decreased abundance of Bifidobacterium Breve in extremely preterm infants (gestational age <28 weeks) compared to moderate preterm infants (gestational age 29-32 weeks). Supplementation with probiotics decreased Acinetobacter and increased Bifidobacterium in the gut of preterm neonates regardless of gestational age.

Conclusion

Gestational age and probiotic supplementation alter the gut microbiota of preterm infants admitted to the NICU.

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

Effect of Feeding Fresh or Frozen Breast Milk on the Gut Microbiota of Premature Infants: A Prospective Observational Study

BACKGROUND

Breast milk is essential for premature infants. It contains a variety of functional and protective nutrients that help to create a suitable microenvironment for intestinal development and maturation. This prospective and observational study was planned to examine the effects of feeding premature infants with fresh or frozen breastmilk on their gut microbiota.

MATERIALS AND METHODS

The study was carried out with a total of 40 infants, with a gestational age of 28-326 weeks, fed fresh (n = 20) or frozen (n = 20) breastmilk. Stool samples were stored at -80°C until analysis. Infants were included in groups based on the feed type, which accounted for more than 70% of their 10-day feeding. The Mann-Whitney U, Chi-square, and t-tests were used to evaluate the demographic data. Stool samples were analyzed by sequencing the V3--V4 region of the 16S rRNA gene from the extracted DNA for microbiota analysis.

RESULTS

Streptococcus and Enterobacteriales, the majority of which are considered human pathogens, in infants receiving frozen breastmilk (Streptococcus 69%, Enterobacteriales 79%) was higher than that in infants receiving fresh breastmilk (Streptococcus 16%, Enterobacteriales 49%). Further, the Lactobacillus and Bifidobacterium species were more abundant in infants who received fresh breastmilk (Lactobacillus 17%, Bifidobacterium 12%) than in infants who received frozen breastmilk (Lactobacillus 3%, Bifidobacterium 1%).

CONCLUSION

Thus, compared to frozen breast milk, fresh breastmilk has an effect on the diversity of preterm infants' gut microbiota.

Efficacy and Safety of Bifidobacterium longum Supplementation in Infants: A Meta-Analysis of Randomized Controlled Trials

BACKGROUND

Strategies to stabilize and support overall infant health by increasing the number of Bifidobacterium longum in the infant gut are of interest, but few studies have systematically addressed this issue. We aimed to evaluate the efficacy and safety of Bifidobacterium longum use in infants using meta-analysis.

METHODS

We searched PubMed, EMBASE, Cochrane Library of Systematic Reviews, and SinoMed for publications until 27 July 2022. The main outcomes of interest were weight gain, risk of necrotizing enterocolitis (NEC), and adverse events. Two authors independently performed study screening, risk of bias assessment, and data extraction. Outcome data were extracted from each included study and combined using mean difference (MD) or risk ratio (RR) and finally combined using a fixed-effect model or random-effect model.

RESULTS

A total of 4481 relevant studies were identified, of which 15 were found to be eligible for randomized controlled trials and were included in the meta-analysis. The combined extracted data showed that the intervention group containing Bifidobacterium longum had a significantly lower risk of NEC (RR = 0.539, 95% CI: 0.333, 0.874) compared to the control group. There was no statistical difference between the intervention and control groups regarding weight gain (MD = 0.029, 95% CI: -0.032, 0.090), the occurrence of adverse events (RR = 0.986, 95% CI: 0.843, 1.153), and serious adverse events (RR = 0.881, 95% CI: 0.493, 1.573).

CONCLUSIONS

Bifidobacterium longum may significantly reduce the risk of NEC in infants as well as being safe; thus, further research evidence is needed on whether there is a benefit on weight gain.

Changes in Gut Microbiota at 1-60 Days in 92 Preterm Infants in a Neonatal Intensive Care Unit Using 16S rRNA Gene Sequencing

BACKGROUND Neonatal gut diversity is influenced by birth conditions and probiotic/antibiotic use. The gut microbiota affects brain development, immunity, and risk of diseases. Preterm infants, especially in neonatal intensive care units (NICUs), have different gut flora from full-term infants, suggesting in utero microbial colonization. This study examined gut microbiota changes in 92 NICU preterm infants in China. MATERIAL AND METHODS We collected data on 92 preterm infants admitted to the NICU immediately after birth, and fecal samples were collected on days 1, 3, 7, 14, 21, 28, and 60. We analyzed changes in intestinal bacteria through 16S rRNA sequencing, predicted the change in gut microbiota function over time, and compared the effects of main feeding modality on the intestinal bacteria of preterm infants. RESULTS At the phylum level, the top 5 phyla in total accounted for 99.69% of the abundance, in decreasing order of abundance: Proteobacteria, Firmicutes, Actinobacteria, Tenericutes, and Bacteroidetes. At the genus level, the top 10 genera in terms of abundance accounted for a total of 90.90%, in decreasing order of abundance: Pseudomonas, Staphylococcus, Klebsiella, Escherichia-Shigella, unclassified Enterobacteriaceae, Staphylococcus, Clostridium-sensu-stricto-1, Streptococcus, Sphingomonas, and Ureaplasma. The abundance of Proteobacteria and Pseudomonas showed a decreasing trend at first, reached a minimum at day 14, and then an increasing trend, while the opposite trend was observed for Firmicutes. The metabolic function of the bacterial community changed greatly at different time points. The abundance of Proteobacteria at the phylum level and Streptococcus at the genus level in formula-fed infants were significantly higher than in breast-fed infants. CONCLUSIONS Between 1 and 60 days, the gut microbiome in preterm infants in the NICU changed with changes in feeding patterns, with the main gut bacteria being from the phyla, Proteobacteria, and Pseudomonas.

The core phageome and its interrelationship with preterm human milk lipids

Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite this, interrelationships between lipids and phages are poorly characterized in preterm HM. Shotgun metagenomics and untargeted lipidomics of phage and lipid profiles from 99 preterm HM samples reveals that phages are abundant and prevalent from the first week and throughout the first 100 days of lactation. Phage-host richness of preterm HM increases longitudinally. Core phage communities characterized by Staphylococcus- and Propionibacterium-infecting phages are significantly correlated with long-chain fatty acid abundances over lactational age. We report here a phage-lipid interaction in preterm HM, highlighting the potential importance of phage carriage in preterm HM. These results reveal possible strategies for phage carriage in HM and their importance in early-life microbiota development.

Gut acquisition of Extended-spectrum β-lactamases-producing Klebsiella pneumoniae in preterm neonates: Critical role of enteral feeding, and endotracheal tubes in the neonatal intensive care unit (NICU)

BACKGROUND

Klebsiella spp. can colonize the intestine of preterm neonates, and over-growth has been associated with necrotizing enterocolitis, hospital-acquired infections, and late-onset sepsis. This could lead us to suggest that the clinical pertinence of intestinal colonization with ESBL in preterm neonates appears to be important. We conducted this study to characterize the genetic proprieties of ESBL-producing Klebsiella pneumoniae (ESBL-KP) under clinical isolates and to describe the risk factors for the intestinal tract acquisition event during hospitalization.

METHODS

One hundred and thirteen premature infants were recruited from the neonatal intensive care unit (NICU). All newborns are issued from the birth suites of the pregnancy department. Two rectal swabs were planned to define K. Pneumoniae intestinal carriage status. ESBL-KP was confirmed by Brilliance ESBL selective chromogenic Agar. Antimicrobial susceptibility testing including phenotypic testing and genotypic detection of the most commonly described ESBL genes was done. Logistic regression models were performed to find the variables associated with the acquisition event of ESBL-KP.

RESULTS

A total of 62 (54.86%) premature neonates were colonized with ESBL-KP. The rate of blaSHV, blaTEM, blaCTX-M1, blaCTX-M2, blaCTX-M9, and blaOXA-48 genes among the isolates was 82, 48, 93.5, 4.8, 11.2 and 3.22%, respectively. We found that ESBLs K. Pneumoniae isolates were 100% resistant to amoxicillin, clavulanic acid-amoxicillin, cefotaxime, ceftazidime, and gentamicin. The regression model is for a given significant association between the tract intestinal of ESBL-KP acquisition events and the use of enteral tube feeding (OR = 38.46, 95% CI: 7.86-188.20, p-Value: 0.001), and endotracheal tubes (OR = 4.86, 95% CI: 1.37-17.19, p-Value 0.014).

CONCLUSION

Our finding supposes that the enteral feeding tube and endotracheal tube might have a critical role in colonizing the intestinal tract of preterm infants. This highlights the current status of both practices that will require updated procedures in the NICU.

Risk factors and predictive models for early recurrent intussusception in children: a retrospective cohort study

Background

Early recurrent intussusception (ERI) in children is common and seriously affects the physical and mental health of the children. There are few reports discussing risk factors for ERI in children, and this study aims to identify risk factors for ERI in children and build predictive models.

Methods

We conducted a retrospective study of 787 children with no relapse intussusception (NRI) and 82 children with ERI between January 2011 and December 2021. Univariate and multifactorial stepwise logistic regression analysis was used to analyze the correlation between 11 factors and ERI, to determine the independent risk factors for ERI in children. The prediction model was established by independent risk factors and then verified.

Results

Age, vomiting, bloody stools, and monocyte ratios were independently correlated with the composite endpoint (P<0.05). A nomogram was constructed and a calibration curve was plotted, using independent risk factors. Based on the disease's diagnostic score, the predictive model's performance was validated by using logistic regression receiver operating characteristic (ROC) curve detection, with area under the curve (AUC) value of 0.883 [95% confidence interval (CI): 0.846-0.920], and the calibration curve was close to the ideal diagonal line. In addition, the decision curve analysis (DCA) showed that the model had significant net benefits.

Conclusions

Independent risk factors for ERI in children are age, vomiting, bloody stool, and monocyte ratio. Children older than 1 year in age, who lacked vomiting and bloody stool symptoms, and who exhibited an elevated ratio of monocytes were more likely to relapse early. The predictive model constructed herein can predict the early recurrence of children with ERI, providing a reference for clinicians' individualized judgments.

Neonatal outcomes following introduction of routine probiotic supplementation to very preterm infants

AIM

To evaluate the combined outcome of death and/or severe grade necrotising enterocolitis (NEC) in very preterm infants admitted to Cork University Maternity Hospital, Ireland, before and after introduction of routine supplementation with Bifidobacterium bifidum and Lactobacillus acidophilus probiotics (Infloran®).

METHODS

A retrospective study of infants <32 weeks gestation and < 1500 g surviving beyond 72 h of life was performed. Two 6-year epochs; pre-probiotics (Epoch 1: 2008-2013) and with probiotics (Epoch 2: 2015-2020), were evaluated. The primary outcome was defined as death after 72 h or NEC Bell stage 2a or greater.

RESULTS

Seven-hundred-and-forty-four infants were included (Epoch 1: 391, Epoch 2: 353). The primary outcome occurred in 67 infants (Epoch 1: 37, Epoch 2: 30, p = 0.646). After adjustment, the difference was significant (OR [95% CI]: 0.53 [0.29 to 0.97], p = 0.038). Differences between epochs did not depend on gestational age group (<28 weeks; ≥28 weeks).

CONCLUSION

There was an associated reduction of the composite outcome of severe grade NEC and/or death, after adjustment for confounding variables, with introduction of routine administration of a B. bifidum and L. acidophilus probiotic at our institution.

Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness

Introduction

Associative connections have previously been identified between nasopharyngeal infections and infant mortality. The nasopharyngeal microbiome may potentially influence the severity of these infections.

Methods

We conducted an analysis of a longitudinal prospective cohort study of 1,981 infants who underwent nasopharyngeal sampling from 1 week through 14 weeks of age at 2-3-week intervals. In all, 27 microbiome samples from 9 of the infants in the cohort who developed fatal acute febrile illness (fAFI) were analyzed in pooled comparisons with 69 samples from 10 healthy comparator infants. We completed 16S rRNA amplicon gene sequencing all infant NP samples and characterized the maturation of the infant NP microbiome among the fAFI(+) and fAFI(-) infant cohorts.

Results

Beta diversity measures of fAFI(-) infants were markedly higher than those of fAFI(+) infants. The fAFI(+) infant NP microbiome was marked by higher abundances of Escherichia, Pseudomonas, Leuconostoc, and Weissella, with low relative presence of Alkalibacterium, Dolosigranulum, Moraxella, and Streptococcus.

Conclusions

Our results suggest that nasopharyngeal microbiome dysbiosis precedes fAFI in young infants. Early dysbiosis, involving microbes such as Escherichia, may play a role in the causal pathway leading to fAFI or could be a marker of other pathogenic forces that directly lead to fAFI.

Longitudinal observational study protocol - Preterm Infants: Microbiome Establishment, Neuro-CrossTalk and Origins (PIMENTO)

INTRODUCTION

Very preterm infants are at risk of abnormal microbiome colonisation in the first weeks to months of life. Several important associated factors have been identified including gestational age, mode of delivery, antibiotic exposure and feeding. Preterm infants are at risk of a number of pathologies for which the microbiome may play a central role, including necrotising enterocolitis and sepsis. The objective of this study is to determine detailed microbiome changes that occur around implementation of different management practices including empiric antibiotic use, advancement of feeds and administration of probiotics during admission to the neonatal intensive care unit.

METHODS AND ANALYSIS

A single-site, longitudinal observational study of infants born less than 32 weeks gestation, including collection of maternal samples around delivery and breastmilk and infant samples from admission through discharge from the neonatal unit.

ETHICS AND DISSEMINATION

The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals.The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases.

TRIAL REGISTRATION NUMBER

NCT05803577.

Microbial associations and transfers across the One Health Triad effects on human and animal adiposity and temperament: a protocol for an observational pilot study

Introduction

It is known that humans and pet dogs harbor microbial communities that are important regulators of health and disease. Pet dogs have been shown to promote microbial exchange between members of a household, a process that may have lasting health implications. Infancy marks a unique period of development as environmental exploration and introduction to complementary foods occur. This may lead to greater opportunities for microbial transfer between pet dogs and human infants due to a more confined shared environment, similar means of mobility, greater physical contact, and increased frequency of shared foods. This human-animal bond has led to extensive research in the areas of childhood allergies and behavioral health; however, there is a paucity in the available literature that has evaluated how this unique ecological relationship may impact both human and animal health.

Methods

Infants who reside in a household with a pet dog will be recruited from the greater Phoenix metropolitan area for this longitudinal, observational pilot study and followed through the complementary feeding period. Infant and pet dog fecal, salivary, and skin samples, as well as environmental samples from feeding areas/surfaces and main indoor play areas from both infants and pet dogs will be collected through in-home visits before (~5 mos), during (~9 mos), and after (~12 mos) the complementary feeding (CF) period. Anthropometrics, temperament, and dietary habits of both infants and pet dogs along with assessment of the home condition will also be collected. Microbial comparisons between infant and pet dog samples and evaluation of microbial changes during the CF period will be evaluated. Further, we will assess relationships between microbial composition and adiposity and temperament of both infants and pet dogs.

Discussion

The proposed observational pilot study will advance the available science by exploring how microbial communities are associated and change between infants and pet dogs before, during, and after the CF period, a unique period of human growth and development. Findings from this study will provide insights into the impact these ecological relationships have on each other and how transfer across the One Health Triad impacts human and animal health.

Conserved Covarying Gut Microbial Network in Preterm Infants and Childhood Growth During the First 5 Years of Life: A Prospective Cohort Study

BACKGROUND

Longitudinally conserved microbe-microbe interactions may provide insights to understand the complex dynamic system of early-life gut microbiota among preterm infants.

OBJECTIVES

We aimed to profile the covarying network of gut microbiota among preterm infants and investigate its potential influence on host growth (2-5 y).

METHODS

We collected time-series stool samples (n = 717 from children and n = 116 from mothers) among 51 preterm and 51 full-term infants from birth up to 5 y of age and among 53 mothers. The included infants underwent time-series measurements of early-life gut microbiota (0-5 y) and growth (2-5 y) from June 2014 to April 2017. The covarying taxa that exhibited consistent covariation from day 1 to year 5 were defined as conserved features in the development of gut microbiota. Childrens' height-for-age z score (HAZ) and weight-for-age z score were calculated according to World Health Organization Child Growth Standards.

RESULTS

We observed distinct dynamic patterns of both microbial alpha and beta diversity comparing preterm infants with full-term controls during the very early stage (<3 mo). Moreover, we identified a covarying network containing 10 taxa as a conserved gut microbial feature of these preterm infants from birth to 5 y old. This covarying network was distinctive between preterm and full-term infants before 3 mo of age (P < 0.001) and tended to be similar as the infants grew up. Several covarying taxa of the network during early life (<3 mo) were associated with childhood growth (2-5 y) (eg, Clostridium_sensu_stricto_1 with HAZ, β = -0.32, q < 0.01), and the human milk feeding duration was a main modulating factor.

CONCLUSIONS

Preterm born children possess conserved and distinct covarying microbiota during very early life, which may have a profound influence on their growth later in life. This trial was registered at clinicaltrials.gov as NCT03373721.

Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS

Background

Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance.

Methods

In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period.

Results

The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii, Cutibacterium acnes, Staphylococcus haemolyticus, Pseudomonas aeruginosa, and Enterococcus faecium. Acinetobacter baumannii, particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples.

Conclusion

The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.

Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life

Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of the above-mentioned factors on the premature-born infants' respiratory metagenome or more generally its maturation is unknown. We therefore applied shotgun metagenome sequencing of oropharyngeal swabs to analyze the airway metagenome development of 24 preterm infants from one week postpartum to 15 months of age. Beta diversity analysis revealed a distinct clustering of airway microbial communities from hospitalized preterms and samples after hospital discharge. At nine and 15 months of age, the preterm infants lost their hospital-acquired individual metagenome signatures towards a common taxonomic structure. However, ecological network analysis and Random Forest classification of cross-sectional data revealed that by this age the preterm infants did not succeed in establishing the uniform and stable bacterial community structures that are characteristic for healthy full-term infants.

Infection control measures against multidrug-resistant Gram-negative bacteria in children and neonates

The increase in infections caused by multidrug-resistant (MDR) Gram-negative bacteria in neonatal and pediatric intensive care units over recent years is alarming. MDR Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii have constituted the main causes of the MDR Gram-negative bacteria problem. The implementation of infection control measures such as hand hygiene, cohorting of patients, contact precautions, active surveillance and environmental cleaning could diminish their spread. Recently, water safety has been identified as a major component of infection control policies. The aim of the current review is to highlight the effectiveness of these infection control measures in managing outbreaks caused by MDR Gram-negative bacteria in neonatal and pediatric intensive care units and highlight future perspectives on the topic.

Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile

Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p > 0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater's initial disposal may have helped the native soil microbial community recover.

Microbial diversity in the vaginal microbiota and its link to pregnancy outcomes

The vaginal microbiota refers to the microorganisms that reside in the vagina. These microorganisms contribute significantly to a woman's reproductive and general health. A healthy vaginal microbiota is typically a low-diversity environment with a predominance of lactic acid-producing Lactobacillus species. Factors such as antibiotic use, sexual activity, and hormonal changes can disrupt the balance of the vaginal microbiota, leading to conditions such as bacterial vaginosis. The composition of the vaginal microbiota changes and takes on added importance during pregnancy, serving as a barrier against infection for both mother and fetus. Despite the importance of the microorganisms that colonize the vagina, details of how changes in composition and diversity can impact pregnancy outcomes is poorly understood. This is especially true for woman with a high prevalence of Gardnerella vaginalis. Here we report on a diverse cohort of 749 women, enrolled in the InSPIRe cohort, during their final trimester of pregnancy. We show that Lactobacilli, including L. crispatus are important in maintaining low diversity, and that depletion in this critical community is linked with preterm delivery. We further demonstrate that it is overall diversity of the vaginal microbiota, not specific species, which provides the best indicator of risk.

Serratia marcescens Colonization in a Neonatal Intensive Care Unit Has Multiple Sources, with Sink Drains as a Major Reservoir

Compelling evidence suggests a contribution of the sink environment to the transmission of opportunistic pathogens from the hospital environment to patients in neonatal intensive care units (NICU). In this study, the distribution of the opportunistic pathogen Serratia marcescens in the sink environment and newborns in a NICU was investigated. More than 500 sink drain and faucet samples were collected over the course of five sampling campaigns undertaken over 3 years. Distribution and diversity of S. marcescens were examined with a modified MacConkey medium and a high-throughput short-sequence typing (HiSST) method. Sink drains were an important reservoir of S. marcescens, with an average of 44% positive samples, whereas no faucet sample was positive. The genotypic diversity of S. marcescens was moderate, with an average of two genotypes per drain, while the spatial distribution of S. marcescens was heterogeneous. The genotypic profiles of 52 clinical isolates were highly heterogeneous, with 27 unique genotypes, of which 71% of isolates were found in more than one patient. S. marcescens acquisition during the first outbreaks was mainly caused by horizontal transmissions. HiSST analyses revealed 10 potential cases of patient-to-patient transmission of S. marcescens, five cases of patient-to-sink transmission, and one bidirectional transfer between sink and patient. Environmental and clinical isolates were found in sink drains up to 1 year after the first detection, supporting persisting drain colonization. This extensive survey suggests multiple reservoirs of S. marcescens within the NICU, including patients and sink drains, but other external sources should also be considered. IMPORTANCE The bacterium Serratia marcescens is an important opportunistic human pathogen that thrives in many environments, can become multidrug resistant, and is often involved in nosocomial outbreaks in neonatal intensive care units (NICU). We evaluated the role of sinks during five suspected S. marcescens outbreaks in a NICU. An innovative approach combining molecular and culture methods was used to maximize the detection and typing of S. marcescens in the sink environment. Our results indicate multiple reservoirs of S. marcescens within the NICU, including patients, sink drains, and external sources. These results highlight the importance of sinks as a major reservoir of S. marcescens and potential sources of future outbreaks.

Used Nasogastric Feeding Tubes from Neonates Contain Infant-Specific Bacterial Profiles

Nasogastric feeding tubes (NG-tubes) from neonates contain potentially pathogenic bacteria. Using culture-based techniques, we have previously determined that the usage duration of NG-tubes did not impact the colonization of the nasogastric tubes. In the present study, we performed 16S rRNA gene amplicon sequencing to evaluate the microbial profile of 94 used nasogastric tubes collected from a single neonatal intensive care unit. Using culture-based whole genome sequencing, we as-sessed whether the same strain persisted in NG-tubes collected from the same neonate across different time-points. We found that the most commonly occurring Gram-negative bacteria were Enterobacteriaceae, Klebsiella and Serratia, while the most common Gram-positive bacteria were staphylococci and streptococci. The microbiota of the NG-feeding tube was overall infant-specific, rather than dependent on the duration of use. Furthermore, we determined that reoccurring species from the individual infant represented the same strain and that several strains were common for more than one infant. Our findings indicate that bacterial profiles found in NG-tubes of neonates are host-specific, not dependent on the duration of use and strongly influenced by the environment.

Burnham CA, Warner BB, Tarr PI, Dantas G. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit

Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.

SNV-FEAST: microbial source tracking with single nucleotide variants

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

Impact of the mother's gut microbiota on infant microbiome and brain development

The link between the gut microbiome and health has recently garnered considerable interest in its employment for medicinal purposes. Since the early microbiota exhibits more flexibility compared to that of adults, there is a considerable possibility that altering it will have significant consequences on human development. Like genetics, the human microbiota can be passed from mother to child. This provides information on early microbiota acquisition, future development, and prospective chances for intervention. The succession and acquisition of early-life microbiota, modifications of the maternal microbiota during pregnancy, delivery, and infancy, and new efforts to understand maternal-infant microbiota transmission are discussed in this article. We also examine the shaping of mother-to-infant microbial transmission, and we then explore possible paths for future research to advance our knowledge in this area.

Rapid Evaluation of Staple Placement in Stabilized α Helices Using Bacterial Surface Display

There are a wealth of proteins involved in disease that cannot be targeted by current therapeutics because they are inside cells, inaccessible to most macromolecules, and lack small-molecule binding pockets. Stapled peptides, where two amino acids are covalently linked, form a class of macrocycles that have the potential to penetrate cell membranes and disrupt intracellular protein-protein interactions. However, their discovery relies on solid-phase synthesis, greatly limiting queries into their complex design space involving amino acid sequence, staple location, and staple chemistry. Here, we use stabilized peptide engineering by Escherichia coli display (SPEED), which utilizes noncanonical amino acids and click chemistry for stabilization, to rapidly screen staple location and linker structure to accelerate peptide design. After using SPEED to confirm hotspots in the mdm2-p53 interaction, we evaluated different staple locations and staple chemistry to identify several novel nanomolar and sub-nanomolar antagonists. Next, we evaluated SPEED in the B cell lymphoma 2 (Bcl-2) protein family, which is responsible for regulating apoptosis. We report that novel staple locations modified in the context of BIM, a high affinity but nonspecific naturally occurring peptide, improve its specificity against the highly homologous proteins in the Bcl-2 family. These compounds demonstrate the importance of screening linker location and chemistry in identifying high affinity and specific peptide antagonists. Therefore, SPEED can be used as a versatile platform to evaluate multiple design criteria for stabilized peptide engineering.

The interplay between human papillomavirus and vaginal microbiota in cervical cancer development

Over the past few decades, we have grown accustomed to the idea that human papillomavirus can cause tumors. The genetic and environmental factors that make the difference between elimination of viral infection and the development of cancer are therefore an area of active investigation at present. Microbiota has emerged as an important factor that may affect this balance by increasing or decreasing the ability of viral infection to promote. The female reproductive system has its specific microbiota that helps to maintain health and prevent infection with pathogens. In contrast to other mucosal sites, the vaginal microbiota typically has low diversity and contains few Lactobacillus spp. which by using high-throughput 16s rRNA gene sequencing, classified into five different community state types. According to emerging information, increased diversity of vaginal microbiota and reduced abundance of Lactobacillus spp. contribute to HPV acquisition, persistence, and development of cervical cancer. In this review, the role of normal female reproductive tract microbiota in health, mechanisms which dysbiosis can cause diseases through interaction with microbes and several therapeutic approaches were addressed.

Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership

BACKGROUND

Many animals and plants acquire their coevolved symbiotic partners shortly post-embryonic development. Thus, during embryogenesis, cellular features must be developed that will promote both symbiont colonization of the appropriate tissues, as well as persistence at those sites. While variation in the degree of maturation occurs in newborn tissues, little is unknown about how this variation influences the establishment and persistence of host-microbe associations.

RESULTS

The binary symbiosis model, the squid-vibrio (Euprymna scolopes-Vibrio fischeri) system, offers a way to study how an environmental gram-negative bacterium establishes a beneficial, persistent, extracellular colonization of an animal host. Here, we show that bacterial symbionts occupy six different colonization sites in the light-emitting organ of the host that have both distinct morphologies and responses to antibiotic treatment. Vibrio fischeri was most resilient to antibiotic disturbance when contained within the smallest and least mature colonization sites. We show that this variability in crypt development at the time of hatching allows the immature sites to act as a symbiont reservoir that has the potential to reseed the more mature sites in the host organ when they have been cleared by antibiotic treatment. This strategy may produce an ecologically significant resiliency to the association.

CONCLUSIONS

The data presented here provide evidence that the evolution of the squid-vibrio association has been selected for a nascent organ with a range of host tissue maturity at the onset of symbiosis. The resulting variation in physical and chemical environments results in a spectrum of host-symbiont interactions, notably, variation in susceptibility to environmental disturbance. This "insurance policy" provides resiliency to the symbiosis during the critical period of its early development. While differences in tissue maturity at birth have been documented in other animals, such as along the infant gut tract of mammals, the impact of this variation on host-microbiome interactions has not been studied. Because a wide variety of symbiosis characters are highly conserved over animal evolution, studies of the squid-vibrio association have the promise of providing insights into basic strategies that ensure successful bacterial passage between hosts in horizontally transmitted symbioses. Video Abstract.

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine

Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterize fecal samples of 55 infants (<1500 g, n = 383, female = 22) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses; targeted 16S rRNA gene sequencing and shotgun metagenomics), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids (German Registry of Clinical Trials, No.: DRKS00009290). Regimens including probiotic Bifidobacterium longum subsp. infantis NCDO 2203 supplementation affect microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of NCDO 2203 is associated with a substantial reduction of microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus LCR 35 or no supplementation. Crucially, the beneficial effects of Bifidobacterium longum subsp. infantis NCDO 2203 supplementation depends on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on development and maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.

A High Dose of Dietary Berberine Improves Gut Wall Morphology, Despite an Expansion of Enterobacteriaceae and a Reduction in Beneficial Microbiota in Broiler Chickens

Phytogenic products are embraced as alternatives to antimicrobials, and some are known to mitigate intestinal inflammation and ensure optimal gut health and performance in broiler chickens. Dietary inclusion of berberine, a benzylisoquinoline alkaloid found in plants, is believed to exert gut health-promoting effects through modulation of the gut microbiota; however, there are only a few studies investigating its effects in chickens. The aim of this study was to investigate the interplay between dietary supplementation of a high concentration of berberine, the gastrointestinal microbiota, and histomorphological parameters in the gut. Berberine was shown to increase villus length and decrease crypt depth and CD3⁺ T-lymphocyte infiltration in the gut tissue of chickens at different ages. Berberine affected the diversity of the gut microbiota from the jejunum to the colon, both at a compositional and functional level, with larger effects observed in the large intestine. A high concentration of berberine enriched members of the Enterobacteriaceae family and depleted members of the Ruminococcaceae, Lachnospiraceae, and Peptostreptococcaceae families, as well as tended to reduce butyrate production in the cecum. In vivo results were confirmed by in vitro growth experiments, where increasing concentrations of berberine inhibited the growth of several butyrate-producing strains while not affecting that of Enterobacteriaceae strains. Positive correlations were found between berberine levels in plasma and villus length or villus-to-crypt ratio in the jejunum. Our study showed that berberine supplementation at a high concentration improves chicken gut morphology toward decreased inflammation, which is likely not mediated by the induced gut microbiota shifts. IMPORTANCE Dietary additives are widely used to reduce intestinal inflammation and enteritis, a growing problem in the broiler industry. Berberine, with anti-inflammatory, antioxidant, and antimicrobial activity, would be an interesting feed additive in this regard. This study investigates for the first time the impact of berberine supplementation on the chicken gastrointestinal microbiota, as a potential mechanism to improve gut health, together with histological effects in the small intestine. This study identified a dose-effect of berberine on the gut microbiota, indicating the importance of finding an optimal dose to be used as a dietary additive.

Therapeutic Potential of Gut Microbiota and Its Metabolite Short-Chain Fatty Acids in Neonatal Necrotizing Enterocolitis

Short chain fatty acids (SCFAs), the principle end-products produced by the anaerobic gut microbial fermentation of complex carbohydrates (CHO) in the colon perform beneficial roles in metabolic health. Butyrate, acetate and propionate are the main SCFA metabolites, which maintain gut homeostasis and host immune responses, enhance gut barrier integrity and reduce gut inflammation via a range of epigenetic modifications in DNA/histone methylation underlying these effects. The infant gut microbiota composition is characterized by higher abundances of SCFA-producing bacteria. A large number of in vitro/vivo studies have demonstrated the therapeutic implications of SCFA-producing bacteria in infant inflammatory diseases, such as obesity and asthma, but the application of gut microbiota and its metabolite SCFAs to necrotizing enterocolitis (NEC), an acute inflammatory necrosis of the distal small intestine/colon affecting premature newborns, is scarce. Indeed, the beneficial health effects attributed to SCFAs and SCFA-producing bacteria in neonatal NEC are still to be understood. Thus, this literature review aims to summarize the available evidence on the therapeutic potential of gut microbiota and its metabolite SCFAs in neonatal NEC using the PubMed/MEDLINE database.

Release of HMGB1 and Toll-like Receptors 2, 4, and 9 Signaling Are Modulated by Bifidobacterium animalis subsp. lactis BB-12 and Salmonella Typhimurium in a Gnotobiotic Piglet Model of Preterm Infants

Gnotobiotic (GN) animals with defined microbiota allow us to study host-microbiota and microbiota-microbiota interferences. Preterm germ-free (GF) piglets were mono-associated with probiotic Bifidobacterium animalis subsp. lactis BB-12 (BB12) to ameliorate/prevent the consequences of infection with the Salmonella Typhimurium strain LT2 (LT2). Goblet cell density; expression of Toll-like receptors (TLRs) 2, 4, and 9; high mobility group box 1 (HMGB1); interleukin (IL)-6; and IL-12/23p40 were analyzed to evaluate the possible modulatory effect of BB12. BB12 prevented an LT2-induced decrease of goblet cell density in the colon. TLRs signaling modified by LT2 was not influenced by the previous association with BB12. The expression of HMGB1, IL-6, and IL12/23p40 in the jejunum, ileum, and colon and their levels in plasma were all decreased by BB12, but these changes were not statistically significant. In the colon, differences in HMGB1 distribution between the GF and LT2 piglet groups were observed. In conclusion, the mono-association of GF piglets with BB12 prior to LT2 infection partially ameliorated the inflammatory response to LT2 infection.

Changes in vaginal microbiome after focused ultrasound treatment of high-risk human papillomavirus infection-related low-grade cervical lesions

BACKGROUND

In this study, the changes of vaginal microbiome after focused ultrasound (FU) treatment were evaluated to explore the possible mechanism of FU in the treatment of high-risk human papillomavirus (HR-HPV) infection.

METHODS

This study was nested in the FU arm of a prospective cohort study. A total of 37 patients diagnosed with HR-HPV infection-related cervical low-grade squamous intraepithelial lesion (LSIL) who met the inclusion criteria were enrolled in this study from October 2020 to November 2021, and these patients were treated with FU. We used 16S ribosomal RNA (16S rRNA) gene amplicon sequencing to profile the vaginal microbiota composition of patients before and 3 months after FU treatment.

RESULTS

After FU treatment, HR-HPV was cleared in 24 patients, with a clearance rate of 75.0% (24/32). Lactobacillus iners was the predominant species among all samples. No significant difference was found in alpha-diversity index before and 3 months after FU treatment (P > 0.05), but the rarefaction curves showed that the vaginal microbial diversity before FU treatment was higher than that after FU treatment. Linear discriminant analysis (LDA) effect size (LEfSe) showed that Bifidobacterium contributed the most to the difference between the two groups at the genus level, and the abundance after FU treatment was significantly higher than that before treatment (P = 0.000).

CONCLUSIONS

The decrease of vaginal microbial diversity may be related to the clearance of HR-HPV infection, and FU treatment contributed to the decrease of vaginal microbial diversity. Increased Bifidobacterium abundance in the vaginal microbiome may be associated with clearance of HR-HPV infection, and FU treatment may contribute to the increase in Bifidobacterium abundance.

TRIAL REGISTRATION NUMBER

 This study was registered in the Chinese Clinical Trial Registry on 23/11/2020 (ChiCTR2000040162).

Lung Allograft Microbiome Association with Gastroesophageal Reflux, Inflammation, and Allograft Dysfunction

Rationale: It remains unclear how gastroesophageal reflux disease (GERD) affects allograft microbial community composition in lung transplant recipients and its impact on lung allograft inflammation and function. Objectives: Our objective was to compare the allograft microbiota in lung transplant recipients with or without clinically diagnosed GERD in the first year after transplant and assess associations between GERD, allograft microbiota, inflammation, and acute and chronic lung allograft dysfunction (ALAD and CLAD). Methods: A total of 268 BAL samples were collected from 75 lung transplant recipients at a single transplant center every 3 months after transplant for 1 year. Ten transplant recipients from a separate transplant center provided samples before and after antireflux Nissen fundoplication surgery. Microbial community composition and density were measured using 16S ribosomal RNA gene sequencing and quantitative polymerase chain reaction, respectively, and inflammatory markers and bile acids were quantified. Measurements and Main Results: We observed a range of allograft community composition with three discernible types (labeled community state types [CSTs] 1-3). Transplant recipients with GERD were more likely to have CST1, characterized by high bacterial density and relative abundance of the oropharyngeal colonizing genera Prevotella and Veillonella. GERD was associated with more frequent transitions to CST1. CST1 was associated with lower inflammatory cytokine concentrations than pathogen-dominated CST3 across the range of microbial densities observed. Cox proportional hazard models revealed associations between CST3 and the development of ALAD/CLAD. Nissen fundoplication decreased bacterial load and proinflammatory cytokines. Conclusions: GERD was associated with a high bacterial density, Prevotella- and Veillonella-dominated CST1. CST3, but not CST1 or GERD, was associated with inflammation and early development of ALAD and CLAD. Nissen fundoplication was associated with a reduction in microbial density in BAL fluid samples, especially the CST1-specific genus, Prevotella.

A comparison of bacterial colonization between nasogastric and orogastric enteral feeding tubes in infants in the neonatal intensive care unit

OBJECTIVE

Feeding tubes harbor microbial contaminants; studies to date have not explored differences between orogastric (OG) and nasogastric (NG) tube biofilms. We sought to extend a previous analysis by comparing bacterial colonization by location (OG v NG) and by evaluating clinical factors that may affect tube bacterial populations.

STUDY DESIGN

The pharyngeal segments of 41 infant feeding tubes (14 OG and 27 NG) from 41 infants were analyzed by next generation 16 S rRNA sequencing on the MiSeq platform.

RESULTS

At the phylum level, Proteobacteria had the highest relative abundance of both OG and NG tubes. At the genus/species level, nine taxa differed significantly between OG and NG tubes. Alpha and beta diversity analyses showed significant differences between OG and NG tubes with relatively little contribution from clinical factors.

CONCLUSION

The route of feeding tube insertion (oral vs nasal) had a greater impact on bacterial colonization than the assessed clinical factors.

Vaginal microbiome: considerations for reproductive health

The microbial communities are an indispensable part of the human defense system and coexist with humans as symbionts, contributing to the metabolic functions and immune defense against pathogens. An ecologically stable vaginal microbiota is dominated by Lactobacillus species, which plays an important role in the prevention of genital infections by controlling the vaginal pH, reducing glycogen to lactic acid, and stimulating bacteriocins and hydrogen peroxide. In contrast, an abnormal vaginal microbial composition is associated with an increased risk of bacterial vaginosis, trichomoniasis, sexually transmitted diseases, preterm labor and other birth defects. This microbial diversity is affected by race, ethnicity, pregnancy, hormonal changes, sexual activities, hygiene practices and other conditions. In the present review, we discuss the changes in the microbial community of the vaginal region at different stages of a female's life cycle and its influence on her reproductive health and pathological conditions.

Probiotic Use in Preterm Neonates: A Review and Bibliometric Analysis

Background: Necrotizing enterocolitis (NEC) is a major health burden in peterm neonates with mortality rates between 21% and 50%. Prophylaxis is of primary importance as early diagnosis is hindered by the lack of specific signs and laboratory markers. Although probiotics have been routinely used for NEC prophylaxis in neonatal intensive care units around the world, clinical trials provide contradictory data, which fuels an ongoing debate about their efficacy and safety.

Aims: To perform a review and bibliometric analysis on available clinical trials and case reports data on the safety and efficacy of probiotics in preterm neonates and identify relevant publication trends and patterns.

Methods: A bibliometric search for publications on the topic was performed in the Web of Science Core Collection database and the resulting records analyzed in bibliometrix package in R.

Results: Trends in publication activity, historical direct citation network relationships and keyword co-ocurrences were discussed in the context of the most recent therapeutic recommendations.

Conclusion: We took a round view of the potential drawbacks to probiotic use in preterm infants and their possible solutions.