Differences in the human gut microbiota with varying depressive symptom severity scores.

Depression is a prevalent mental health disorder, and its incidence has increased further because of the coronavirus disease 2019 (COVID-19) pandemic. The gut microbiome has been suggested as a potential target for mental health treatment because of the bidirectional communication system between the brain and gastrointestinal tract, known as the gut-brain axis. We aimed to investigate the relationship between the human gut microbiome and depression screening by analyzing the abundance and types of microbiomes among individuals living in Japan, where mental health awareness and support may differ from those in other countries owing to cultural factors. We used a data-driven approach to evaluate the gut microbiome of participants who underwent commercial gut microbiota testing services and completed a questionnaire survey that included a test for scoring depressive tendencies. Our data analysis results indicated that no significant differences in gut microbiome composition were found among the groups based on their depression screening scores. However, the results also indicated the potential existence of a few differentially abundant bacterial taxa. Specifically, the detected bacterial changes in abundance suggest that the Bifidobacteriaceae, Streptococcaceae, and Veillonellaceae families are candidates for differentially abundant bacteria. Our findings should contribute to the growing body of research on the relationship between gut microbiome and mental health, highlighting the potential of microbiome-based interventions for depression treatment. The limitations of this study include the lack of clear medical information on the participants' diagnoses. Future research could benefit from a larger sample size and more detailed clinical information.

Temperament in Early Childhood Is Associated With Gut Microbiota Composition and Diversity.

Temperament is a key predictor of human mental health and cognitive and emotional development. Although human fear behavior is reportedly associated with gut microbiome in infancy, infant gut microbiota changes dramatically during the first 5 years, when the diversity and composition of gut microbiome are established. This period is crucial for the development of the prefrontal cortex, which is involved in emotion regulation. Therefore, this study investigated the relationship between temperament and gut microbiota in 284 preschool children aged 3-4 years. Child temperament was assessed by maternal reports of the Children's Behavior Questionnaire. Gut microbiota (alpha/beta diversity and genera abundance) was evaluated using 16S rRNA sequencing of stool samples. A low abundance of anti-inflammatory bacteria (e.g., Faecalibacterium) and a high abundance of pro-inflammatory bacteria (e.g., Eggerthella, Flavonifractor) were associated with higher negative emotionality and stress response (i.e., negative affectivity, ß = -0.17, p = 0.004) and lower positive emotionality and reward-seeking (i.e., surgency/extraversion, ß = 0.15, p = 0.013). Additionally, gut microbiota diversity was associated with speed of response initiation (i.e., impulsivity, a specific aspect of surgency/extraversion, ß = 0.16, p = 0.008). This study provides insight into the biological mechanisms of temperament and takes important steps toward identifying predictive markers of psychological/emotional risk.

Oral and Intestinal Bacterial Flora in Patients with Increased Periodontal Inflamed Surface Area: A Cross-Sectional Study.

Background/Objectives: Periodontitis is caused by bacterial plaque. The oral microflora may interact with the intestinal microflora and play a role in the development of periodontitis. The periodontal inflamed surface area (PISA) has been shown to be a useful indicator of periodontal disease related to systemic diseases; however, few studies have shown an association between PISA and the bacterial flora. This study aimed to determine the association between PISA and oral and intestinal bacteria. Methods: Participants were recruited between 2018 and 2021 at the Medical and Dental Collaboration Center of Kanagawa Dental University Hospital. A periodontal clinical examination was performed, and the PISA was calculated. Salivary tests were conducted, and leukocyte scores in the saliva were calculated. Moreover, 16S rRNA amplicon sequencing was performed using saliva and stool samples to analyze oral and intestinal bacteria, respectively. Results: Higher PISA levels resulted in an increased presence of Bacteroides and a decreased presence of Proteobacteria and Actinobacteria in the saliva. An increase in Bacteroides was detected in the saliva of patients with high leukocyte scores. No correlation was observed between PISA and intestinal bacteria. Conclusions: Bacteroides was highly abundant in the saliva of patients with worsened periodontal conditions, as indicated by PISA. No association was found between PISA and intestinal bacteria.

Intestinal microbiome and maternal mental health: preventing parental stress and enhancing resilience in mothers.

The number of mothers suffering from mental illness is increasing steadily, particularly under conditions of the coronavirus pandemic. The identification of factors that contribute to resilience in mothers is urgently needed to decrease the risks of poor physical and psychological health. We focused on the risk of parenting stress and psychological resilience in healthy mothers with no psychiatric and physical disorders and conducted two studies to examine the relationships between intestinal microbiota, physical condition, and psychological state. Our results showed that alpha diversity and beta diversity of the microbiome are related to high parenting stress risk. Psychological resilience and physical conditions were associated with relative abundances of the genera Blautia, Clostridium, and Eggerthella. This study helps further understand the gut-brain axis mechanisms and supports proposals for enhancing resilience in mothers.

Gut microbial stability in older Japanese populations: insights from the Mykinso cohort.

Gut microbiota imbalance plays an important role in the pathogenesis of various diseases. Here, we determined microbe-microbe interactions and gut microbiome stability in a Japanese population with varying body mass indices (BMIs) and enterotypes. Using 16S ribosomal RNA gene sequencing, we analyzed gut microbial data from fecal samples obtained from 3,365 older Japanese individuals. The individuals were divided into lean, normal, and obese groups based on their BMIs. They were further categorized according to their gut microbiota enterotypes: Bacteroides (enterotype B), Prevotella (enterotype P), and Ruminococcus (enterotype R). We obtained data on different host factors, such as age, BMI, and disease status, using a survey questionnaire evaluated by the Mykinso gut microbiome testing service. Subsequently, we evaluated the co-occurrence network. Individual differences in BMI were associated with differences in co-occurrence networks. By exploring the network topology based on BMI status, we observed that the network density was lower in the lean group than that in the normal group. Furthermore, a simulation-based stability analysis revealed a lower resistance index in the lean group than those in the other two groups. Our results provide insights into various microbe-microbe interactions and gut microbial stability and could aid in developing appropriate therapeutic strategies targeting gut microbiota modulation to manage frailty.

Altered Gut Microbiota Composition Is Associated with Difficulty in Explicit Emotion Regulation in Young Children.

Executive function (EF) consists of explicit emotion regulation (EER) and cognitive control (CC). Childhood EER in particular predicts mental and physical health in adulthood. Identifying factors affecting EER development has implications for lifelong physical and mental health. Gut microbiota (GM) has attracted attention as a potential biomarker for risk of physical and mental problems in adulthood. Furthermore, GM is related to brain function/structure, which plays a crucial role in emotional processing. However, little is known about how GM compositions are associated with the development of emotion regulation in early childhood. Therefore, in this study, we examined 257 children aged 3-4 to investigate links between GM and risk to EF. EF was measured using the Mother-Reported Behavior Rating Inventory of Executive Function-Preschool version. GM composition (alpha/beta diversity and genus abundance) was evaluated using 16S rRNA gene sequencing and compared between EF-risk and non-risk groups. Our results show that children with EER-risk (an index of inhibitory self-control) had a higher abundance of the genera Actinomyces and Sutterella. Although we have not established a direct link between GM and CC risk, our findings indicate that GM of preschoolers is closely associated with emotional processing and that EERrisk children have more inflammation-related bacteria.

Prolonged gut microbial alterations in post-transplant survivors of allogeneic haematopoietic stem cell transplantation.

Dysbiosis of the gut microbiota has been reported to increase early complications after allogeneic haematopoietic stem cell transplantation (allo-HSCT). However, it remains unclear whether gut microbial alterations persist during late complications, such as chronic graft-versus-host disease (cGVHD) or secondary cancers. Here, we analysed the gut microbiota of 59 patients who survived for 1-21.7 years (median, 6.4 years) after allo-HSCT. Long-term survivors showed lower gut microbial diversity than the age- and sex-matched healthy controls. This decreased diversity was reflected in the reduced abundance of the butyrate-producing bacteria. Patients with a history of grade 3 acute graft-versus-host disease (aGVHD) exhibited higher Veillonella abundance than patients with a history of grade 1-2 or non-aGVHD cases. The abundance of Faecalibacterium showed no decrease only in limited cGVHD cases. Additionally, the microbial structure in the secondary cancer group was significantly different (p < 0.05) from that in the non-secondary cancer group. This study is the first to show that microbial dysbiosis is present over a 10-year lifetime after discharge following allo-HSCT. Our results suggest that these prolonged gut microbial alterations may be associated with the development and exacerbation of late complications in post-transplant survivors.

Average gut flora in healthy Japanese subjects stratified by age and body mass index.

Imbalance of the gut microbiota plays an important role in the pathogenesis of various diseases. Although many clinical studies have analyzed the gut microbiota, the definition of normal gut microbiota remains unclear. In this study, we aim to establish the average gut microbiota in the healthy Japanese population. Using 16S ribosomal RNA gene sequencing, we analyzed gut microbial data from fecal samples obtained from 6,101 healthy Japanese individuals. Based on their ages, the individuals were divided into three groups: young, middle-age, and old. Individuals were further categorized according to body mass index (BMI) into lean, normal, and obese groups. The α and ß diversities in the old group were significantly higher than those in the young and middle-age groups. The Firmicutes/Bacteroidetes ratio of subjects in the obese category was significantly lower compared with those of subjects in the lean and normal categories in the young and middle-age groups. Genus Bacteroides was the dominant gut microbiota across all the BMI categories in all the age groups. Among the top ten genera, the abundances of Bacteroides, Bifidobacterium, Anaerostipes, Blautia, Dorea, Fusicatenibacter, Lachnoclostridium, and Parabacteroides were significantly lower in the old group than in the young and middle-age groups. The correlation network at the genus level revealed different microbe-microbe interactions associated with age and BMI. We determined the average Japanese gut microbiota, and this information could be used as a reference. The gut microbiota greatly differs based on the life stage and metabolic status of the host, and this gives rise to a variety of host-gut microbe interactions that can lead to an increased susceptibility to disease.

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.

BACKGROUND: 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol. RESULTS: QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data. CONCLUSIONS: These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.

A cross-sectional analysis from the Mykinso Cohort Study: establishing reference ranges for Japanese gut microbial indices.

The purpose of this study was to establish reference ranges for gut microbial indices by collecting real-world Japanese microbiome data from a Mykinso cohort. Although several large cohort studies have focused on the human gut microbiome, large cohort studies of the gut microbiome from Japanese populations are scarce, especially from healthy or non-diseased individuals. We collected stool samples and original survey lifestyle information from 5,843 Japanese individuals through the Mykinso gut microbiome testing service. From the obtained 16S rRNA sequence data derived from stool samples, the ratio and distribution of each taxon were analyzed. The relationship between different epidemiological attributes and gut microbial indicators were statistically analyzed. The qualitative and quantitative indicators of these common gut microbiota were confirmed to be strongly correlated with age, sex, constipation/diarrhea, and history of lifestyle-related diseases. Therefore, we set up a healthy sub-cohort that controlled for these attribute factors and defined reference ranges from the distribution of gut microbial index in that population. Taken together, these results show that the gut microbiota of Japanese people had high beta-diversity, with no single "typical" gut microbiota type. We believe that the reference ranges for the gut microbial indices obtained in this study can be new reference values for determining the balance and health of the gut microbiota of an individual. In the future, it is necessary to clarify the clinical validity of these reference values by comparing them with a clinical disease cohort.

Usefulness of Machine Learning-Based Gut Microbiome Analysis for Identifying Patients with Irritable Bowels Syndrome.

Irritable bowel syndrome (IBS) is diagnosed by subjective clinical symptoms. We aimed to establish an objective IBS prediction model based on gut microbiome analyses employing machine learning. We collected fecal samples and clinical data from 85 adult patients who met the Rome III criteria for IBS, as well as from 26 healthy controls. The fecal gut microbiome profiles were analyzed by 16S ribosomal RNA sequencing, and the determination of short-chain fatty acids was performed by gas chromatography-mass spectrometry. The IBS prediction model based on gut microbiome data after machine learning was validated for its consistency for clinical diagnosis. The fecal microbiome alpha-diversity indices were significantly smaller in the IBS group than in the healthy controls. The amount of propionic acid and the difference between butyric acid and valerate were significantly higher in the IBS group than in the healthy controls (p < 0.05). Using LASSO logistic regression, we extracted a featured group of bacteria to distinguish IBS patients from healthy controls. Using the data for these featured bacteria, we established a prediction model for identifying IBS patients by machine learning (sensitivity >80%; specificity >90%). Gut microbiome analysis using machine learning is useful for identifying patients with IBS.

Identifying the inserted locus of randomly integrated expression plasmids by whole-genome sequencing of Aspergillus strains.

Whole-genome sequencing was conducted on two Aspergillus oryzae strains used for the manufacturing of food enzymes, Acrylaway® and Shearzyme®, with the aim of identifying the inserted locus of randomly integrated expression plasmid and obtaining flanking sequences for safety assessment. Illumina paired-end sequencing was employed, and the obtained reads were mapped to two references: the public genome sequence of Aspergillus oryzae RIB40 and the in-house sequence of the used expression plasmid. Introducing the concept of linking-reads, one locus for each was successfully identified as the integrated site. In the case of Acrylaway®, the obtained sequences suggested that the expression plasmid had been integrated as multiple copies in tandem form. In the case of Shearzyme®, however, information on one edge of the insert was missing, which required extra polymerase chain reaction (PCR) cloning for safety assessment. A 4-kb deletion was detected at the integrated site. There was also evidence of rearrangement occurring in Shearzyme® strain.

Slowed Dynamics of Thin Filament Regulatory Units Reduces Ca2+-Sensitivity of Cardiac Biomechanical Function.

Actomyosin kinetics in both skinned skeletal muscle fibers at maximum Ca2+-activation and unregulated in vitro motility assays are modulated by solvent microviscosity in a manner consistent with a diffusion limited process. Viscosity might also influence cardiac thin filament Ca2+-regulatory protein dynamics. In vitro motility assays were conducted using thin filaments reconstituted with recombinant human cardiac troponin and tropomyosin; solvent microviscosity was varied by addition of sucrose or glucose. At saturating Ca2+, filament sliding speed (s) was inversely proportional to viscosity. Ca2+-sensitivity (pCa50 ) of s decreased markedly with elevated viscosity (η/η0 ≥ ~1.3). For comparison with unloaded motility assays, steady-state isometric force (F) and kinetics of isometric tension redevelopment (kTR ) were measured in single, permeabilized porcine cardiomyocytes when viscosity surrounding the myofilaments was altered. Maximum Ca2+-activated F changed little for sucrose ≤ 0.3 M (η/η0 ~1.4) or glucose ≤ 0.875 M (η/η0 ~1.66), but decreased at higher concentrations. Sucrose (0.3 M) or glucose (0.875 M) decreased pCa50 for F. kTR at saturating Ca2+ decreased steeply and monotonically with increased viscosity but there was little effect on kTR at sub-maximum Ca2+. Modeling indicates that increased solutes affect dynamics of cardiac muscle Ca2+-regulatory proteins to a much greater extent than actomyosin cross-bridge cycling.

Interaction between troponin and myosin enhances contractile activity of myosin in cardiac muscle.

Ca(2+) signaling in striated muscle cells is critically dependent upon thin filament proteins tropomyosin (Tm) and troponin (Tn) to regulate mechanical output. Using in vitro measurements of contractility, we demonstrate that even in the absence of actin and Tm, human cardiac Tn (cTn) enhances heavy meromyosin MgATPase activity by up to 2.5-fold in solution. In addition, cTn without Tm significantly increases, or superactivates sliding speed of filamentous actin (F-actin) in skeletal motility assays by at least 12%, depending upon [cTn]. cTn alone enhances skeletal heavy meromyosin's MgATPase in a concentration-dependent manner and with sub-micromolar affinity. cTn-mediated increases in myosin ATPase may be the cause of superactivation of maximum Ca(2+)-activated regulated thin filament sliding speed in motility assays relative to unregulated skeletal F-actin. To specifically relate this classical superactivation to cardiac muscle, we demonstrate the same response using motility assays where only cardiac proteins were used, where regulated cardiac thin filament sliding speeds with cardiac myosin are >50% faster than unregulated cardiac F-actin. We additionally demonstrate that the COOH-terminal mobile domain of cTnI is not required for this interaction or functional enhancement of myosin activity. Our results provide strong evidence that the interaction between cTn and myosin is responsible for enhancement of cross-bridge kinetics when myosin binds in the vicinity of Tn on thin filaments. These data imply a novel and functionally significant molecular interaction that may provide new insights into Ca(2+) activation in cardiac muscle cells.

Enhanced active cross-bridges during diastole: molecular pathogenesis of tropomyosin's HCM mutations.

Three HCM-causing tropomyosin (Tm) mutants (V95A, D175N, and E180G) were examined using the thin-filament extraction and reconstitution technique. The effects of Ca(2+), ATP, phosphate, and ADP concentrations on cross-bridge kinetics in myocardium reconstituted with each of these mutants were studied at 25°C, and compared to wild-type (WT) Tm at physiological ionic strength (200 mM). All three mutants showed significantly higher (2-3.5 fold) low Ca(2+) tension (T(LC)) and stiffness than WT at pCa 8.0. High Ca(2+) tension (T(HC)) was significantly higher for E180G than that for WT, whereas T(HC) of V95A and D175N was similar to WT; high Ca(2+) stiffness (Y(HC)) had the same trend. The Ca(2+) sensitivity of isometric force was significantly greater for V95A and E180G than for WT, whereas that of D175N remained the same as for WT; for all mutants, cooperativity was lower than for WT. Nine kinetic constants and the cross-bridge distribution were deduced using sinusoidal analysis. The number of force-generating cross bridges was similar among the D175N, E180G, and WT Tm forms, but it was significantly larger in the case of V95A than WT. We conclude that the increased number of actively cycling cross bridges at pCa 8 is the major cause of Tm mutation-related HCM pathogenesis, which may result in diastolic dysfunction. Decreased contractility (T(act)) in V95A and D175N may further contribute to the severity of myocyte hypertrophy and related prognosis of the disease.