Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age.

Very low birth weight (VLBW) infants (<1500 g) are at risk for poor neurodevelopmental outcomes depending on gestational age (GA), birth weight (BW), and morbidity in early life. The contribution of the gut microbiome is not well understood. Stool samples were collected weekly in the neonatal intensive care unit (NICU) from 24 VLBW infants for 6 weeks after admission and then again at 2 and 4 years of age. The Battelle Development Inventory-2 Screening Test (BDI-2 ST) was administered at 2- and 4-year time points. VLBW infants had dysbiotic microbiota in the NICU that progressed for most to an adult-type microbiota by 4 years of age. The BDI-2 ST results at age of 2 years triggered referral for further testing in 14 toddlers (70%), and by 4 years of age only seven of these 14 continued to require referral. Both NICU infant stool diversity and particular microbial amplicon sequence variants were associated with BDI-2 ST subscales, particularly for cognition, adaptive, and communication subscales, when controlled for GA, BW, and antibiotic exposure. Network analysis of the NICU infant stool microbial ecology showed differences in children needing neurodevelopmental referral. The results of this preliminary study indicate that the neonatal gut microbiome plays a role in early cognitive and behavioral neurodevelopment.

Intestinal Microbiome in Preterm Infants Influenced by Enteral Iron Dosing.

OBJECTIVES: The aim of the study was to compare the intestinal microbiome in very low birth weight (VLBW) infants who received different enteral iron supplementation (EIS) doses. STUDY DESIGN: Longitudinal stool collection in 80 VLBW infants were conducted up to 2 months postnatally in a prospective study. The 16S rRNA regions V4 was used to calculate microbiome compositions and the Piphillin software was used for bacterial functional prediction. Linear mixed effect models and Wilcoxon rank-sum tests were performed to examine the relationships between initial EIS dosage and stool microbiome and bacterial functional potential. RESULTS: There were 105 samples collected before and 237 collected after EIS started from infants with birth gestational age and weight of 28.1 ±â€Š2.4 weeks and 1103 ±â€Š210 g, respectively. The average postnatal age at start of EIS was 17.9 ±â€Š6.9 days and the average initial EIS dose was 4.8 ±â€Š1.1 mg ·â€Škg-1 ·â€Šday-1. Infants who were started on ≥6 mg ·â€Škg-1 ·â€Šday-1 had higher abundances of Proteus and Bifidobacterium and a lower alpha diversity than those started on lower doses (P < 0.05). Infants given higher EIS doses had higher bacterial predicted functional potentials for ferroptosis and epithelial invasion after 2 weeks post EIS. CONCLUSIONS: Higher EIS dosage is linked to higher abundances of Proteus and Bifidobacterium, and a less diverse microbiome and higher predicted potential of bacterial epithelial invasion. These observational findings should be further studied in a randomized study to elucidate the optimal dosage of EIS in VLBW infants.

Gut microbiota perturbation is associated with acute sleep disturbance among rectal cancer patients.

Cancer treatment-associated gut microbial perturbation/dysbiosis has been implicated in the pathobiology of sleep disturbance; however, evidence is scarce. Eighteen newly diagnosed rectal cancer patients (ages 52-81 years; 10 males) completed a sleep disturbance questionnaire and provided stool samples for 16s RNA gene sequencing during chemo-radiotherapy. Descriptive statistics, Wilcoxon test and regression analyses were computed. Regression analyses showed the Shannon's diversity index to be a significant factor associated with sleep disturbance. This preliminary work suggests that the biological "gut-brain axis" mechanism may be associated with symptoms of sleep disturbance.

Association of common genetic variants with human skin color variation in Indian populations.

OBJECTIVES: Human skin color is one of the most conspicuously variable physical traits that has attracted the attention of physical anthropologists, social scientists and human geneticists. Although several studies have established the underlying genes and their variants affecting human skin color, they were mostly confined to Europeans and Africans and similar studies in Indian populations have been scanty. Studying the association between candidate genetic variants and skin color will help to validate previous findings and to better understand the molecular mechanism of skin color variation. METHODS: In this study, 22 candidate SNPs from 12 genes were tested for association with skin color in 299 unrelated samples sourced from nine geographical locations in India. RESULTS: Our study establishes the association of 9 SNPs with the phenotype in Indian populations and could explain ∼31% of the variance in skin color. Haplotype analysis of chromosome 15 revealed a significant association of alleles G, A and C of SNPs rs1426654, rs11070627, and rs12913316, respectively, to the phenotype, and accounted for 17% of the variance. Latitude of the sampling location was also a significant factor, contributing to ∼19% of the variation observed in the samples. CONCLUSIONS: These observations support the findings that rs1426654 and rs4775730 located in SLC24A5, and rs11070627 and rs12913316 located in MYEF2 and CTXN2 genes respectively, are major contributors toward skin pigmentation and would aid in further unraveling the genotype-phenotype association in Indian populations. These findings can be utilized in forensic DNA applications for criminal investigations.

Selective enrichment of STRs for applications in forensic human identification.

Forensic human identification (HID) is currently based on determining repeat length polymorphisms located in short tandem repeat regions in the human genome. Despite the great progress made in the area of multiplex PCR-based approaches, limitations associated with challenging forensic samples such as DNA degradation, cooccurrence of inhabited microbial DNA and PCR inhibitors significantly affect the success rate of human DNA profiling. We have developed a sequence-specific pre-PCR STR enrichment method and evaluated its efficacy using DNA samples doped with various contaminants in view of its application on compromised forensic samples. This strategy has enabled us to generate complete and reproducible DNA profiles from samples doped with fivefold excess of nonhuman DNA and three to fourfold excess of various potent PCR inhibitors than that is claimed to be tolerated by some of the widely used commercial multiplex STR kits, from as little as two nanograms of degraded human DNA. The "hybrid capture"-based STR enrichment strategy described in this study is easily adaptable and offers a sensitive, efficient, and economical approach for successful human DNA profiling from compromised and recalcitrant forensic samples that are usually encountered in mass disaster incidents and missing persons' identifications.

A pilot study: Validation of dried blood spots (DBS) to assess SARS-CoV2 IgG antibody immunoassays in underserved minority population.

Underserved, low-income, rural and certain migrant populations have greater risks and higher incidences of Coronavirus disease 2019 (COVID-19) than more privileged populations. Current in-person testing methods have limitations, namely exposure risk, a requirement of accessible transportation to healthcare facilities, and economic barriers. Dried blood spots (DBS) samples are widely used for diagnostics in many infectious diseases including Rabies, HIV, Ebola viruses and newborn screening. Our goal was to determine the accuracy and reliability of measuring COVID-19 IgG in DBS compared to paired plasma samples in a population with known infection status and then apply this method to screen an underserved minority population with high risk for COVID-9 infection (unvaccinated, pregnant, low income, Hispanic women). To optimize the assay, we tested 22 nonpregnant women, 12 with positive prior PCR testing for SARS-CoV2 infection and 10 with negative PCR results. After the assay was optimized, we tested the assay in a vulnerable population with a high risk for infection, who were 52 Hispanic pregnant women without prior PCR testing or vaccination. DBS assay results in both groups showed an agreement of 100% with paired plasma samples. The availability of a DBS assay could enable people who may not have access or transportation to healthcare facilities to use DBS as a COVID-19 testing vehicle.

A Preliminary Study Exploring the Relationship between Occupational Health Hazards and Gut Microbiota among Firefighters.

Firefighters are exposed to occupational hazards and have a higher prevalence of health issues. The gut microbiota plays a crucial role in the immune, endocrine, and neural systems, and disruptions in its composition can impact health outcomes. This pilot study aimed to investigate the potential association between occupational factors, changes in gut microbiota, and the development of adverse health outcomes in firefighters. To test this hypothesis, we recruited 15 firefighters and age/sex-matched controls to investigate the relationship between occupational environment and gut microbiota. Firefighters exhibit lower intestinal bacterial alpha diversity and a higher presence of pathogenic bacteria than the control. Moreover, unique gut bacterial taxa were observed in firefighters with high post-traumatic stress disorder (PTSD) scores, which could contribute to immune dysregulation and higher susceptibility to pathogen colonization. These preliminary findings suggest that occupational factors, including exposure to traumatic stressors and chemicals, may influence firefighters' health by modulating their gut microbiota. The observed changes in gut microbiota composition and the potential link to occupational hazards highlight the need for further research in larger sample-size studies. Understanding the role of gut microbiota in firefighter health may have implications for preventive measures and interventions to mitigate occupational health risks and improve overall well-being.

Premature Infant Gut Microbiome relationships with childhood behavioral scales: preliminary insights.

Introduction: Very Low Birth Weight (VLBW) infants, born weighing less than 1,500 grams, are at risk for both gut dysbiosis and later neuropsychological developmental deficits. Behavioral effects, while related to neurodevelopment, are often more subtle and difficult to measure. The extent of later neurobehavioral consequences associated with such microbial dysbiosis has yet to be determined. We explored associations between the infants' gut microbiome and early childhood behavior at 4 years of age and identified the bacterial taxa through a multivariate analysis by linear models. Methods: Parents completed the Child Behavior Checklist (CBCL) focused on different DSM diagnostic categories: affective, anxiety, pervasive developmental, attention deficit/hyperactivity, and oppositional defiant. All the CBCL scores were corrected for gender, delivery method, gestational age, infant birth weight, occurrence of sepsis, and days on antibiotics prior statistical analyses. Canonical correlation analysis (CCA) was performed to determine the relationship between early life gut microbiome and the adjusted CBCL scores. The association of bacterial Amplicon sequence Variants (ASVs) to the CBCL scores were tested with multivariate analysis by linear models (MaAsLin). Results: Nineteen children who were previously born with very low birth weight and studied while hospitalized in the Neonatal Intensive Care Unit (NICU) were included in this study. Statistically significant associations were observed between early life gut bacteria such as Veillonella dispar, Enterococcus, Escherichia coli, and Rumincococcus to later behavior at 4 years. No significant association could be observed with early-life gut microbiome alpha diversity and behavioral measures at 4 years. Discussion: These preliminary observational data provide insight into the relationships between VLBW gut microbiome dysbiosis and childhood behavior. This study contributes to the literature on gut microbiome analysis by examining various behavioral domains using a standardized tool linked to the Diagnostic and Statistical Manual of Mental Disorders (DSM).

Periodontitis and cardiovascular risk factors in subjects with and without type 1 diabetes: A cross sectional analysis.

AIMS: This cross-sectional analysis explored the relationships between periodontal disease (PD) and subclinical CVD in a cohort of patients with type 1 diabetes and non-diabetic controls. METHODS: Data were collected from adults enrolled in the Coronary Artery Calcification in Type 1 Diabetes (CACTI) study or enrolled through the Barbara Davis Center for Diabetes Adult Clinic. A clinical periodontal exam measured attachment loss and probing depth. Brachial artery distensibility (brachD), carotid intima-media thickness (cIMT), and pulse wave velocity (PWV) were assessed as measures of subclinical cardiovascular structure and function. RESULTS: 144 participants with T1D and 148 non-diabetics were enrolled. Compared to non-diabetic controls, T1D participants had a higher probing depth (2.6 mm vs. 2.5 mm; p = 0.04), higher attachment loss (2.7 mm vs. 2.4 mm; p < 0.01), lower brachD (mean 5.8 vs. 6.4 mmHg; p < 0.01), a higher cIMT (mean 0.68 vs. 0.64 mm; p < 0.01), and a higher PWV (mean 8.3 vs. 7.8 m/s; p < 0.01). There were no significant associations between PD and CVD metrics. CONCLUSIONS: Periodontal and cardiovascular health was worse in participants with T1D compared to non-diabetics. No significant associations between PD measures and CVD were identified.

Postnatal growth and gut microbiota development influenced early childhood growth in preterm infants.

Background: Preterm infants are at high risk for growth failure and childhood weight problems due to the disruption of normal intrauterine growth and nutrition. Early nutritional support and microbiome acquisition can play an important role in childhood growth. Objective: Our study examined potential postnatal indicators, including gut bacterial compositions, macronutrients, and catch-up growth, of growth pattern from infancy into early childhood. Methods: This is a retrospective study of preterm infants born < 35 weeks who were followed up in the university complex care clinic from 2012-2018. Weight and length z-scores at birth, 1, 2, 4, 6, 12 and 15 months, and body mass index (BMI) and length z-scores from 2 to 5 years of age were collected. Catch-up growths were calculated by changes in z-scores and divided into early (birth-4 months) and late (4-18 months). Postnatal nutritional data and fecal samples were collected. Fecal microbiome data obtained from 16S RNA V4 sequencing was analyzed against clinical and growth data using a regression model. Results: 160 infants included in the final analysis had birth weight and gestational age of 1,149 ± 496 grams and 28 ± 3 weeks. Early weight gain positively correlated with length z-scores but not with BMI at 2 years of age. BMI at 2 years of age strongly correlated with BMI at 3, 4, and 5 years of age. Postnatal abundance of Gammaproteobacteria was negatively associated with early growth while Bacteroides and Lactobacillus were positively associated with childhood BMI. Conclusion: Our findings suggest that optimal postnatal nutrition promoted early catch-up growth in weight as well as improved linear growth without influence on childhood BMI. Postnatal gut microbial colonization, which is a modifiable factor, was associated with childhood growth in preterm infants.

Linking the oral microbiome and salivary cytokine abundance to circadian oscillations.

Saliva has immense potential as a diagnostic fluid for identification and monitoring of several systemic diseases. Composition of the microbiome and inflammation has been associated and reflective of oral and overall health. In addition, the relative ease of collection of saliva further strengthens large-scale diagnostic purposes. However, the future clinical utility of saliva cannot be fully determined without a detailed examination of daily fluctuations that may occur within the oral microbiome and inflammation due to circadian rhythm. In this study, we explored the association between the salivary microbiome and the concentration of IL-1ß, IL-6 and IL-8 in the saliva of 12 healthy adults over a period of 24 h by studying the 16S rRNA gene followed by negative binomial mixed model regression analysis. To determine the periodicity and oscillation patterns of both the oral microbiome and inflammation (represented by the cytokine levels), two of the twelve subjects were studied for three consecutive days. Our results indicate that the Operational Taxonomic Units (OTUs) belonging to Prevotella, SR1 and Ruminococcaceae are significantly associated to IL-1ß while Prevotella and Granulicatella were associated with IL-8. Our findings have also revealed a periodicity of both the oral microbiome (OTUs) and inflammation (cytokine levels) with identifiable patterns between IL-1ß and Prevotella, and IL-6 with Prevotella, Neisseria and Porphyromonas. We believe that this study represents the first measure and demonstration of simultaneous periodic fluctuations of cytokine levels and specific populations of the oral microbiome.

The Association between Early-Life Gut Microbiota and Long-Term Health and Diseases.

Early life gut microbiota have been increasingly recognized as major contributors to short and/or long-term human health and diseases. Numerous studies have demonstrated that human gut microbial colonization begins at birth, but continues to develop a succession of taxonomic abundances for two to three years until the gut microbiota reaches adult-like diversity and proportions. Several factors, including gestational age (GA), delivery mode, birth weight, feeding types, antibiotic exposure, maternal microbiome, and diet, influence the diversity, abundance, and function of early life gut microbiota. Gut microbial life is essential for assisting with the digestion of food substances to release nutrients, exerting control over pathogens, stimulating or modulating the immune system, and influencing many systems such as the liver, brain, and endocrine system. Microbial metabolites play multiple roles in these interactions. Furthermore, studies provide evidence supporting that imbalances of the gut microbiota in early life, referred to as dysbiosis, are associated with specific childhood or adult disease outcomes, such as asthma, atopic dermatitis, diabetes, allergic diseases, obesity, cardiovascular diseases (CVD), and neurological disorders. These findings support that the human gut microbiota may play a fundamental role in the risk of acquiring diseases that may be programmed during early life. In fact, it is critical to explore the role of the human gut microbiota in early life.

Changes in Gut Microbiome Associated With Co-Occurring Symptoms Development During Chemo-Radiation for Rectal Cancer: A Proof of Concept Study.

PURPOSE: To examine a) whether there are significant differences in the severity of symptoms of fatigue, sleep disturbance, or depression between patients with rectal cancer who develop co-occurring symptoms and those with no symptoms before and at the end of chemotherapy and radiation therapy (CRT); b) differences in gut microbial diversity between those with co-occurring symptoms and those with no symptoms; and c) whether before-treatment diversity measurements and taxa abundances can predict co-occurrence of symptoms. METHODS: Stool samples and symptom ratings were collected from 31 patients with rectal cancer prior to and at the end of (24-28 treatments) CRT. Descriptive statistics were computed and the Mann-Whitney U test was performed for symptoms. Gut microbiome data were analyzed using R's vegan package software. RESULTS: Participants with co-occurring symptoms reported greater severity of fatigue at the end of CRT than those with no symptoms. Bacteroides and Blautia2 abundances differed between participants with co-occurring symptoms and those with no symptoms. Our random forest classification (unsupervised learning algorithm) predicted participants who developed co-occurring symptoms with 74% accuracy, using specific phylum, family, and genera abundances as predictors. CONCLUSION: Our preliminary results point to an association between the gut microbiota and co-occurring symptoms in rectal cancer patients and serves as a first step in potential identification of a microbiota-based classifier.

Giuffrè-Tsukahara syndrome: Evidence for X-linked dominant inheritance and review.

We report on a girl with Giuffrè-Tsukahara syndrome manifesting microcephaly, mental retardation, radio-ulnar synostosis, short stature and scoliosis. Skewed X-inactivation was not observed in our patient. We reviewed previous reports and provide evidence in support of X-linked dominant inheritance of this condition.

The genetic affinities of Gujjar and Ladakhi populations of India.

The Union Territories of Jammu and Kashmir (J&K) and Ladakh in North India owing to their unique geographic location offer a wide variety of landscape from plains to high altitudes and is a congruence of many languages and cultural practices. Here, we present the genetic diversity studies of Gujjars from Jammu region of J&K and Ladakhi population based on a battery of autosomal single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome. These two populations were observed to be genetically distant to each other as well as to other populations from India. Interestingly, Y-STR analyses showed a closer affinity of Gujjars to other nomadic populations of Pashtuns from Baghlans and Kunduz provinces of Afghanistan and Pashtuns and Sindhis of Pakistan. Gujjars exhibited lesser genetic diversity as compared to Ladakhi population. M30f and M9 were the most abundant mitochondrial haplogroups observed among Gujjars and Ladakhis, respectively. A lower matrilineal to patrilineal diversity was observed for both these populations. The current study presents the first comprehensive analysis of Gujjars and Ladakhis and reveals their unique genetic affiliations with other populations of the world.

Gut Microbiota and Immune System Interactions.

Dynamic interactions between gut microbiota and a host's innate and adaptive immune systems play key roles in maintaining intestinal homeostasis and inhibiting inflammation. The gut microbiota metabolizes proteins and complex carbohydrates, synthesize vitamins, and produce an enormous number of metabolic products that can mediate cross-talk between gut epithelial and immune cells. As a defense mechanism, gut epithelial cells produce a mucosal barrier to segregate microbiota from host immune cells and reduce intestinal permeability. An impaired interaction between gut microbiota and the mucosal immune system can lead to an increased abundance of potentially pathogenic gram-negative bacteria and their associated metabolic changes, disrupting the epithelial barrier and increasing susceptibility to infections. Gut dysbiosis, or negative alterations in gut microbial composition, can also dysregulate immune responses, causing inflammation, oxidative stress, and insulin resistance. Over time, chronic dysbiosis and the translocation of bacteria and their metabolic products across the mucosal barrier may increase prevalence of type 2 diabetes, cardiovascular disease, inflammatory bowel disease, autoimmune disease, and a variety of cancers. In this paper, we highlight the pivotal role gut microbiota and their metabolites (short-chain fatty acids (SCFAs)) play in mucosal immunity.

Correction: Yoo, J.Y., et al. Gut Microbiota and Immune System Interactions. Microorganisms 2020, 8, 1587.

Corrections have been made to "Gut Microbiota and Immune System Interactions" [...].

Predicted Metabolic Pathway Distributions in Stool Bacteria in Very-Low-Birth-Weight Infants: Potential Relationships with NICU Faltered Growth.

Many very-low-birth-weight (VLBW) infants experience growth faltering in early life despite adequate nutrition. Early growth patterns can affect later neurodevelopmental and anthropometric potentials. The role of the dysbiotic gut microbiome in VLBW infant growth is unknown. Eighty-four VLBW infants were followed for six weeks after birth with weekly stool collection. DNA was extracted from samples and the V4 region of the 16S rRNA gene was sequenced with Illumina MiSeq. A similar microbiota database from full-term infants was used for comparing gut microbiome and predicted metabolic pathways. The class Gammaproteobacteria increased or remained consistent over time in VLBW infants. Out of 228 metabolic pathways that were significantly different between term and VLBW infants, 133 pathways were significantly lower in VLBW infants. Major metabolic differences in their gut microbiome included pathways involved in decreased glycan biosynthesis and metabolism, reduced biosynthetic capacity, interrupted amino acid metabolism, changes that could result in increased infection susceptibility, and many other system deficiencies. Our study reveals poor postnatal growth in a VLBW cohort who had dysbiotic gut microbiota and differences in predicted metabolic pathways compared to term infants. The gut microbiota in VLBW infants likely plays an important role in postnatal growth.

A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations.

India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.

Unraveling the human salivary microbiome diversity in Indian populations.

The importance of studying the salivary microbiome has been highlighted for its connection to health and disease and as a potential tool for supplementing human genetic diversity studies. While the salivary microbiome has been studied in various world populations, Indian populations have not been examined. We therefore analyzed microbiome diversity in saliva samples from 92 volunteers from eight different sampling locations in India by amplifying and sequencing variable regions (V1 and V2) of the bacterial 16S rRNA gene. The results showed immense bacterial richness in Indian populations; we identified 165 bacterial genera and 785 unique Operational Taxonomic Units (OTUs), with substantial sharing among the populations. There were small, but significant correlations in the abundance of bacterial genera in sampling locations from the same geographic region. Most of the core OTUs detected were also observed previously in other populations, but Solobacterium spp., Lachnoanaerobaculum spp. and Alloprevotella spp. were observed to be a component of the saliva microbiome unique to Indian populations. Importantly, nine bacterial genera were observed that were not listed in the Human Oral Microbiome Database (HOMD). These results highlight the importance of analyzing underrepresented populations like those of India.