Dysbiosis of the gut microbiota in children with severe motor and intellectual disabilities receiving enteral nutrition: A pilot study.

BACKGROUND: Children with severe motor and intellectual disabilities (SMIDs) frequently and continuously receive enteral nutrition and medications and lack adequate exercise, which may lead to dysbiosis, an imbalance in the composition of the gut microbiota. However, studies on the composition of gut microbiota in children with SMIDs are limited. Therefore, we aimed to examine the characteristics of the gut microbiota in children with SMIDs. METHODS: 16S rRNA gene sequencing was performed using fecal samples of 10 children with SMIDs, who received enteral nutrition through a gastric fistula or gastric tube (SMID group: median age, 10.0 years), and 19 healthy children (healthy control [HC] group: median age, 9.0 years). Microbial diversity, microbial composition, and abundance of butyric acid-producing bacteria were compared between the groups. Daily dietary fiber intake in the SMID group was evaluated using questionnaires. RESULTS: The Shannon and Simpson indices (alpha diversity indices) were significantly lower in the SMID group than those in the HC group. Beta diversity analysis identified different clusters. Compared with the HC group, Clostridiales and butyric acid-producing bacteria were less abundant and Bacteroidales were more abundant in the SMID group. Dietary fiber intake in the SMID group was approximately two-thirds of the estimated average requirement for healthy Japanese children. CONCLUSION: Children with SMIDs showed dysbiosis with alteration in the microbial diversity, which could partly be attributed to their low dietary fiber intake. Further studies, with the intervention of prebiotics, probiotics, and synbiotics, are warranted to improve dysbiosis in children with SMIDs.

Dysbiosis in Gut Microbiota in Children Born Preterm Who Developed Autism Spectrum Disorder: A Pilot Study.

The gut microbiota was reported to differ between children with autism spectrum disorder (ASD) and typically developing (TD) children, and dysbiosis of the gut microbiota in preterm infants is common. Here, we explored the characteristics of gut microbiota in children born preterm with ASD. We performed 16S rRNA gene sequencing using stool samples from ASD children born preterm and TD children born preterm. Alpha diversity was significantly greater in the ASD group. A comparison of beta diversity showed different clusters. Linear discriminant analysis effect size analysis revealed significantly more Firmicutes in the ASD group compared with the TD group. In conclusion, the gut microbiota in children born preterm differs between children with ASD and TD.

Allele frequencies of 31 autosomal short tandem repeat (auSTR) loci obtained using the Precision ID GlobalFiler™ NGS STR Panel v2 in 322 individuals from the Japanese population.

In human identification methods that target short tandem repeats (STRs), massively parallel sequencing (MPS) technology has made it possible to genotype at the level of the specific sequence itself. This allows for the detection of repeat unit variants and single nucleotide polymorphisms (SNPs) adjacent to the STRs. Using the GlobalFiler™ NGS STR Panel v2, Ion S5, and Converge software, this study constructed a Japanese database of 31 autosomal STRs (auSTRs) and two sex markers from 322 individuals. After excluding some sequence errors and stutters, a total of 31 novel alleles were identified. Additionally, using the allele frequencies of 31 auSTR loci, the match probabilities for the length-based and sequence-based data were calculated to be 1.433 × 10-34 and 9.163 × 10-38, respectively. These values are at least nine orders of magnitude higher than that obtained from 21 auSTR loci in the Japanese population using the conventional capillary electrophoresis method. The database generated in this study is expected to be implemented in forensic practice and used to solve difficult casework.

Removal effect of DNA contamination by hydrogen peroxide plasma compared to ethylene-oxide gas.

We examined the ability of hydrogen peroxide plasma (HPP) to remove DNA contamination, to evaluate whether it is a suitable forensic-grade treatment under ISO 18385. HPP treatment was compared to ethylene-oxide gas (EOG) treatment, which is required by ISO 18385. For the evaluation, commercial control DNA solution and cultured cells sprinkled on Petri dishes were used, and the DNA fragments (214 and 80 bp autosomal DNA fragments and 75 bp Y chromosome fragment) were quantified. HPP treatment was performed up to four times and EOG treatment was performed once. Performing HPP treatment three times was as effective as EOG treatment, with all fragments decreasing to below 1/1,000 in DNA solution. With STR and Y-STR typing, no alleles were detected for three HPP treatments of control DNA using the original amount, i.e., 1 ng. Therefore, HPP appears useful for removing DNA contamination. For cells sprinkled on Petri dishes, the DNA degradation abilities of the HPP and EOG were comparable. However, less DNA was degraded with the HPP and EOG and neither met the ISO criteria. Although the current version of ISO 18385 recommends an evaluation method using cultured cells sprinkled on Petri dishes, it needs to be revised. These findings should be considered when revising ISO 18385.

Development and validation of Kongoh ver. 3.0.1: Open-source software for DNA mixture interpretation in the GlobalFiler system based on a quantitative continuous model.

Probabilistic genotyping software based on continuous models is effective for interpreting DNA profiles derived from DNA mixtures and small DNA samples. In this study, we updated our previously developed Kongoh software (to ver. 3.0.1) to interpret DNA profiles typed using the GlobalFiler™ PCR Amplification Kit. Recently, highly sensitive typing systems such as the GlobalFiler system have facilitated the detection of forward, double-back, and minus 2-nt stutters; therefore, we implemented statistical models for these stutters in Kongoh. In addition, we validated the new version of Kongoh using 2-4-person mixtures and DNA profiles with degradation in the GlobalFiler system. The likelihood ratios (LRs) for true contributors and non-contributors were well separated as the information increased (i.e., larger peak height and fewer contributors), and these LRs tended to neutrality as the information decreased. These trends were observed even in profiles with DNA degradation. The LR values were highly reproducible, and the accuracy of the calculation was also confirmed. Therefore, Kongoh ver. 3.0.1 is useful for interpreting DNA mixtures and degraded DNA samples in the GlobalFiler system.

Association of Neonatal Jaundice with Gut Dysbiosis Characterized by Decreased Bifidobacteriales.

Neonatal jaundice, caused by excess serum bilirubin levels, is a common condition in neonates. Imbalance in the gut microbiota is believed to play a role in the development of neonatal jaundice. Thus, we aimed to reveal the gut microbiota characteristics in neonates with jaundice. 16S rRNA gene sequencing was performed on stool samples collected on day 4 from 26 neonates with jaundice (serum total bilirubin > 15.0 mg/dL) and 17 neonates without jaundice (total serum bilirubin < 10.0 mg/dL). All neonates were born full term, with normal weight, by vaginal delivery, and were breastfed. Neonates who were administered antibiotics, had serum direct bilirubin levels above 1 mg/dL, or had conditions possibly leading to hemolytic anemia were excluded. The median serum bilirubin was 16.0 mg/dL (interquartile range: 15.5-16.8) and 7.4 mg/dL (interquartile range: 6.8-8.3) for the jaundice and non-jaundice groups, respectively. There was no difference in the alpha diversity indices. Meanwhile, in the jaundice group, linear discriminant analysis effect size revealed that Bifidobacteriales were decreased at the order level, while Enterococcaceae were increased and Bifidobacteriaceae were decreased at the family level. Bifidobacteriaceae may act preventatively because of their suppressive effect on beta-glucuronidase, leading to accelerated deconjugation of conjugated bilirubin in the intestine. In summary, neonates with jaundice had dysbiosis characterized by a decreased abundance of Bifidobacteriales.

Fiber-Rich Barley Increases Butyric Acid-Producing Bacteria in the Human Gut Microbiota.

Butyric acid produced in the intestine by butyric acid-producing bacteria (BAPB) is known to suppress excessive inflammatory response and may prevent chronic disease development. We evaluated whether fiber-rich barley intake increases BAPB in the gut and concomitantly butyric acid in feces. Eighteen healthy adults received granola containing functional barley (BARLEYmax®) once daily for four weeks. Fecal DNA before intake, after intake, and one month after intake was analyzed using 16S rRNA gene sequencing to assess microbial diversity, microbial composition at the order level, and the proportion of BAPB. Fecal butyric acid concentration was also measured. There were no significant differences in diversities and microbial composition between samples. The proportion of BAPB increased significantly after the intake (from 5.9% to 8.2%). However, one month after stopping the intake, the proportion of BAPB returned to the original value (5.4%). Fecal butyric acid concentration increased significantly from 0.99 mg/g feces before intake to 1.43 mg/g after intake (p = 0.028), which decreased significantly to 0.87 mg/g after stopping intake (p = 0.008). As BAPB produce butyric acid by degrading dietary fiber, functional barley may act as a prebiotic, increasing BAPB and consequently butyric acid in the intestine.

Evaluation of probability distribution models for stutter ratios in the typing system of GlobalFiler and 3500xL Genetic Analyzer.

As DNA typing systems have become increasingly sensitive in recent years, probability distribution models for back, forward, double-back, and minus 2-nt stutter ratios have been desired to be considered in DNA evidence interpretation using specific software programs. However, experimental investigations have been insufficient, especially for forward, double-back, and minus 2-nt stutters. In this study, we experimentally reevaluated the probability distribution models for each stutter ratio in the typing systems of GlobalFiler™ PCR Amplification Kit and 3500xL Genetic Analyzer from Thermo Fisher Scientific. In addition, to enhance the reliability of longest uninterrupted stretch (LUS) values and corrected allele numbers used in previously developed models for stutter ratios using sequence information (i.e., LUS model and multi-seq model), we propose the weighted average of LUS values and corrected allele numbers based on the number of observations in sequence-based population data. Back stutter ratios demonstrated a positive correlation with allele numbers (allele model) in eight loci, LUS values (LUS model) in eight loci, and corrected allele numbers (multi-seq model) in five loci. The forward stutter ratios (FSRs) of D22S1045 followed the LUS model. FSRs other than D22S1045 and double-back stutter ratios followed the LUS model by considering multiple loci together. Minus 2-nt stutter ratios observed in SE33 and D1S1656 did not increase with the increase in the allele numbers. The adopted models for each stutter ratio can be implemented in software programs for DNA evidence interpretation and enable a reliable interpretation of crime stain profiles in forensic caseworks.

Clinical Significance of Probiotics for Children with Idiopathic Nephrotic Syndrome.

We previously reported that a decrease in butyrate-producing bacteria in the gut is a potential cause of regulatory T cell (Treg) abnormalities in children with idiopathic nephrotic syndrome (INS). Therefore, we hypothesized that administration of butyrate-producing bacteria might reduce INS relapse and the need for immunosuppressants in these patients. Twenty patients in remission from INS (median age 5.3 years, 15 boys) were enrolled in the study and assigned to receive either daily oral treatment with a preparation of 3 g Clostridium butyricum or no probiotic treatment. The number of relapses and requirement for immunosuppressive agents were compared between the two groups. In the probiotic treatment group, analyses of the gut microbiota and Treg measurements were also performed. Probiotic-treated patients experienced fewer INS relapses per year compared with non-probiotic-treated patients (p = 0.016). Further, administration of rituximab in the probiotic treatment group was significantly less frequent compared with the non-probiotic-treated group (p = 0.025). In the probiotic treatment group, analyses before and after probiotic treatment revealed the significant increases in the relative abundance of butyrate-producing bacteria (p = 0.017) and blood Treg counts (p = 0.0065). Thus, oral administration of butyrate-producing bacteria during INS remission may reduce the frequency of relapse and the need for immunosuppressive agents.

Idiopathic nephrotic syndrome in children: role of regulatory T cells and gut microbiota.

BACKGROUND: We investigated whether an association exists between regulatory T cells (Tregs) during initial presentation in children with idiopathic nephrotic syndrome (INS) and later development of frequently relapsing INS. METHODS: Blood samples were obtained at onset and at remission from 25 patients (median age, 4.0 years) with INS; eight did not show relapse after initial response (non-relapsing [NR]), whereas 17 showed frequent relapses (frequently relapsing [FR]). Tregs were measured by flow cytometry; increases were compared between groups. Fecal samples were obtained at onset from 20 patients with INS, as well as from 20 age-matched healthy children. Gut microbiota composition was assessed using 16S ribosomal RNA (rRNA) sequencing (ion PGM). RESULTS: The rate of increase in Tregs from onset to remission was significantly lower in the FR group (124.78%) than in the NR group (879.16%; P < 0.001). Additionally, 16S rRNA sequencing of gut microbiota showed that the proportion of butyric acid-producing bacteria was significantly lower in the FR group (7.08%) than in the healthy children (17.45%; P < 0.001). CONCLUSIONS: In children with INS, small increases in Tregs in response to steroid treatment were associated with subsequent increased risk of frequent relapses. In addition, the FR group had a greater degree of dysbiosis at onset. IMPACT: A low rate of Tregs increase is associated with subsequent frequent relapses of INS. The increase in Tregs in response to steroid treatment was small when dysbiosis was present in patients with INS, particularly when the proportion of butyrate-producing bacteria was considerably reduced We presume that improvement of dysbiosis by administration of probiotics and prebiotics may enhance the rate of Tregs' increase, thus preventing frequent relapse.

Impact of Long-Term Low Dose Antibiotic Prophylaxis on Gut Microbiota in Children.

PURPOSE: We evaluated the effect of long-term low dose antibiotic prophylaxis on children's gut microbiota. MATERIALS AND METHODS: We conducted 16S ribosomal RNA gene sequencing using stool samples from 35 patients younger than 3 years old (median age 5.2 months; male-to-female ratio 17:18) who underwent antibiotic treatment during the acute phase of febrile urinary tract infection. Samples were collected at 5 time points, ie before, during and at 1 to 2, 3 to 4, and 5 to 6 months after febrile urinary tract infection onset and antibiotic treatment. Continuous antibiotic prophylaxis using trimethoprim-sulfamethoxazole was initiated in 23 patients with grade III or higher vesicoureteral reflux and was not administered in 12 patients without reflux. RESULTS: Within 2 weeks after initiation of treatment for febrile urinary tract infection almost all enteric bacteria belonged to the order Lactobacillales, and gut microbiota diversity decreased compared to the pretreatment level (average Shannon index 2.9 before treatment, 1.4 during treatment). The diversity recovered within 1 to 2 months after febrile urinary tract infection onset in both groups. Diversity was maintained during the study period in both groups (p=0.43). A smaller proportion of gut microbiota component belonged to the order Enterobacteriales (p=0.002) in the antibiotic prophylaxis group. CONCLUSIONS: Our results revealed that patients receiving continuous antibiotic prophylaxis had normal gut microbiota diversity, indicating that the effect of trimethoprim-sulfamethoxazole on gut microbiota was insignificant. Furthermore, prophylaxis with trimethoprim-sulfamethoxazole might selectively suppress the growth of bacteria belonging to the order Enterobacteriales, such as Escherichia coli and Klebsiella species, which are the main causative bacteria of febrile urinary tract infections.

Effect of Delivery Mode and Nutrition on Gut Microbiota in Neonates.

BACKGROUND/AIMS: The mode of delivery (vaginal or cesarean section) and feeding type (breastfeeding or formula feeding) of neonates are considered the most influential factors in the development of gut microbiota. OBJECTIVES: This study investigated the effect of prebiotic-rich breast milk on overcoming gut microbiota dysbiosis. METHOD: Stool samples from 36 healthy Japanese neonates were obtained at 4 days and 1 month of age, and divided into 4 groups based on mode of delivery and feeding type. The gut microbiota composition and bacterial diversity were assessed using 16S rRNA sequencing. RESULTS: At 4 days old, vaginally delivered neonates had a significantly higher diversity of bacteria than those born by cesarean section. Bacteroidales and Enterobacteriales were overrepresented in vaginally delivered neonates (p = 0.0031 and p = 0.011), while Bacillales and Lactobacillales were overrepresented in caesarean section delivered neonates (p = 0.012 and p = 0.0016). However, there was little difference in bacterial diversity and bacterial relative abundance at 1 month of age between groups. CONCLUSIONS: Cesarean section delivery appeared to reduce the diversity of neonate gut microbiota, resulting in dysbiosis, but this improved to the equivalent level seen in vaginally delivered infants by 1 month of age. Breastfeeding, even for short periods, may therefore improve neonate gut dysbiosis.

Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles.

It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ±â€¯0.93 in 108 Koreans from Seoul, 8.87 ±â€¯2.89 in 103 Japanese from Tottori, 17.20 ±â€¯3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0-4 Japanese-specific alleles per individual, whereas the Japanese had 4-26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex.

Gut Microbiota Dysbiosis in Children with Relapsing Idiopathic Nephrotic Syndrome.

BACKGROUND: While the etiology of idiopathic nephrotic syndrome (idiopathic nephrotic syndrome [INS]; characterized by repeated relapses and comorbid allergic conditions) remains unknown, recent evidence suggests that dysfunction in regulatory T cells (Tregs) plays an important role in the development of INS as well as allergic diseases. We hypothesized that dysbiosis involving decreased butyric acid-producing gut microbiota leads to defective induction and differentiation of peripherally induced Tregs, resulting in INS relapse. METHODS: Study subjects were 12 children with INS, 8 classified as relapsing (R group; median age: 3.0 years) and 4 as non-relapsing (NR group; median age: 4.3 years), and 11 healthy children (HC group; median age: 5.1 years) serving as normal controls. Measurement of microbiota was performed using 16S ribosomal RNA metagenomic analysis, and fecal butyric acid was measured using high performance liquid chromatography. Flow-cytometric analysis of Tregs and CD4-positive (CD4+) cells in peripheral blood was also performed. RESULTS: Metagenomic analysis of gut microbiota using feces showed that the proportion of butyric acid-producing bacteria was significantly lower in R (median 6.36%) than HC (median 18.84%; p = 0.0013), but no different between NR (median 16.71%) and HC (p = 0.29). Fecal organic acid analysis revealed significantly lower butyric acid quantities in R than HC (medians: 0.48 vs. 0.99 mg/g, p = 0.042). Circulating Tregs as a proportion of CD4+ cells were decreased in 75% of R and NR. CONCLUSION: Pediatric relapsing INS patients show gut microbiota dysbiosis, characterized by a decreased proportion of butyric acid-producing bacteria and lower fecal butyric acid quantities, concomitant with reduced circulatory Tregs.

Investigation of Japanese-specific alleles: most are of Jomon lineage.

Japanese-specific alleles are expected to be powerful markers for the differentiation of the Japanese from other people. In this study, three single nucleotide polymorphisms (SNPs) in the GALNT11, H19, and PLA2G12A genes were analyzed in 2396 DNA samples from 25 global populations, and the derived alleles suggested that Japanese-specific alleles exist on autosomes. To identify new Japanese-specific alleles, candidate SNPs obtained from the HapMap database were investigated using 875 DNA samples from nine populations. A total of 67 (nearly) Japanese-specific derived alleles were observed. Of them, 57 showed higher frequencies in the Ryukyuans, living in the southernmost part of the Japanese Archipelago, than in the Wajins living in mainland Japan, and 43 were also present in Koreans at low frequencies. Jomon skeletons excavated from Hokkaido, the northernmost island of Japan, showed higher frequencies of the three derived alleles in the GALNT11, H19, and PLA2G12A genes than the Ryukyuans, suggesting that most of the 57 derived alleles observed at the high frequencies in the Ryukyuans originated from the Jomon lineage. These novel markers will be useful in the field of forensics.

A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.

Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics.

Examination of seminal stain by HPLC assay of phenolphthalein.

Quantitative high performance liquid chromatography (HPLC) to detect semen was investigated in this study. Briefly, 1cm of a gauze thread with a seminal stain was soaked in the reaction mixture (phenolphthalein diphosphate tetrasodium dissolved in acetate buffer) for 5-10 min, and the supernatant was analyzed by HPLC with a spectrophotometric detector. Phenolphthalein was liberated from the reagent in the presence of acid phosphatase, and the liberated phenolphthalein was detected objectively and was unaffected by blood contamination. Since liberation of phenolphthalein from the reagent occurred slightly in control negative samples, the cut-off value of the examination should be set at 1.0 microg/ml.

Identification of animal species using the partial sequences in the mitochondrial 16S rRNA gene.

This study investigated a PCR direct sequencing method for species identification by analyzing partial sequences in the mitochondrial 16S rRNA genes of many animal species amplified with universal primers. Samples from 182 vertebrates and 103 invertebrates were analyzed, and the sequences could be obtained in 182 and 72 species, respectively. The sequence divergence was sufficient to identify the species at the level of genus with the aid of the GenBank database and the BLAST tool. This method could be a powerful tool for animal species identification, especially in forensic cases in which many unknown biological samples should be analyzed.