Indonesian children fecal microbiome from birth until weaning was different from microbiomes of their mothers

Spatiotemporal patterns of the pregnancy microbiome and links to reproductive disorders

The microbiome of females undergoes extensive remodeling during pregnancy, which is likely to have an impact on the health of both mothers and offspring. Nevertheless, large-scale integrated investigations characterizing microbiome dynamics across key body habitats are lacking. Here, we performed an extensive meta-analysis that compiles and analyzes microbiome profiles from  >10,000 samples across the gut, vagina, and oral cavity of pregnant women from diverse geographical regions. We have unveiled unexpected variations in the taxonomic, functional, and ecological characteristics of microbial communities throughout the course of pregnancy. The gut microbiota showed distinct trajectories between Western and non-Western populations. The vagina microbiota exhibited fluctuating transitions at the genus level across gestation, while the oral microbiota remained relatively stable. We also identified distinctive microbial signatures associated with prevalent pregnancy-related disorders, including opposite variations in the oral and gut microbiota of patients with gestational diabetes and disrupted microbial networks in preterm birth. This study establishes a comprehensive atlas of the pregnancy microbiome by integrating multidimensional datasets and offers foundational insights into the intricate interplay between microbes and host factors that underlie reproductive health.

Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life

The development of infant gut microbiome is a pivotal process affecting the ecology and function of the microbiome, as well as host health. While the establishment of the infant microbiome has been of interest for decades, the focus on gut microbial metabolism and the resulting small molecules (metabolites) has been rather limited. However, technological and computational advances are now enabling researchers to profile the plethora of metabolites in the infant gut, allowing for improved understanding of how gut microbial-derived metabolites drive microbiome community structuring and host-microbial interactions. Here, we review the current knowledge on development of the infant gut microbiota and metabolism within the first year of life, and discuss how these microbial metabolites are key for enhancing our basic understanding of interactions during the early life developmental window.

Effect of the Microbiome on Intestinal Innate Immune Development in Early Life and the Potential Strategy of Early Intervention

Early life is a vital period for mammals to be colonized with the microbiome, which profoundly influences the development of the intestinal immune function. For neonates to resist pathogen infection and avoid gastrointestinal illness, the intestinal innate immune system is critical. Thus, this review summarizes the development of the intestinal microbiome and the intestinal innate immune barrier, including the intestinal epithelium and immune cells from the fetal to the weaning period. Moreover, the impact of the intestinal microbiome on innate immune development and the two main way of early-life intervention including probiotics and fecal microbiota transplantation (FMT) also are discussed in this review. We hope to highlight the crosstalk between early microbial colonization and intestinal innate immunity development and offer some information for early intervention.

Gut Bifidobacterium responses to probiotic Lactobacillus casei Zhang administration vary between subjects from different geographic regions

Bifidobacteria are health-promoting human gut inhabitants, but accurate species-level composition of the gut bifidobacteria and their responses to probiotic intervention have not been fully explored. This was a follow-up work of our previous study, in which 104 volunteers from six different Asiatic regions (Singapore, Indonesia, Xinjiang, Gansu, Inner Mongolia, Mongolia) were recruited. The gut microbiota and their responses towards Lactobacillus casei Zhang (LCZ) intervention were characterized (at days 0, 7, and 14; 14 days after stopping probiotic intake), and region-based differential responses were observed after LCZ intervention. This study further investigated changes in the species-level gut bifidobacteria by PacBio small-molecule real-time sequencing (SMRT) using bifidobacteria-specific primers. Firstly, this study found that Bifidobacterium adolescentis (42.58%) and Bifidobacterium breve (26.34%) were the core species across the six Asiatic regions. Secondly, principal coordinate analysis of probiotic-induced changes in the gut bifidobacterial microbiota (represented by weighted UniFrac distances) grouped the six regions into two clusters, namely northern (Xinjiang, Gansu, Inner Mongolia, and Mongolia) and southern (Singapore, Indonesia) regions. Thirdly, LCZ intervention induced region-based differential responses of gut bifidobacterial microbiota. The relative abundance of Bifidobacterium animalis in subjects from northern but not southern region substantially increased after LCZ intervention. Moreover, LCZ intervention significantly increased the weighted UniFrac distances in the southern but not northern subjects 7 days after LCZ intervention. The gut B. adolescentis correlated significantly and negatively with the weighted UniFrac distances of the baseline gut bifidobacterial microbiota in subjects of northern but not southern region, suggesting a possible homeostatic effect of LCZ on the gut bifidobacterial population of northern but not southern subjects. Collectively, our study found that probiotic-induced responses of the gut bifidobacterial microbiota varied with subjects' geographic origins, and B. adolescentis might play a role in maintaining the overall stability of the gut bifidobacterial population. KEY POINTS: • The core species in the six Asiatic regions are Bifidobacterium adolescentis and Bifidobacterium breve. • The gut bifidobacterial microbiota in people from various geographic origins showed different responses on probiotic administration.

The evolution of dam-litter microbial flora from birth to 60 days of age

Background

Early bacterial colonization in puppies is still a poorly understood phenomenon. Although the topic is of considerable interest, a big gap in knowledge still exists on the understanding of timing and features of neonatal gut colonization. Thence, the purpose of this study was to evaluate the relationship between dam and litter microbial flora, in vaginally delivered puppies, from birth to two months of age. Bacteria were identified using MALDI-TOF, an accurate and sensitive method, and cluster analysis of data provided a new insight on the investigated topic.

Methods

Six dam-litter units of two medium size breeds were enrolled in the study. Vaginal and colostrum/milk samples were collected from dams after delivery and 48h post-partum, while rectal samples were taken from dams and puppies after delivery and at day 2, 30 and 60 (T2, T30 and T60, respectively) post-partum. Bacterial isolation and identification were performed following standard techniques, then the data were analyzed using a new approach based on bacterial genus population composition obtained using a wide MALDI-TOF screening and cluster analysis.

Results

Forty-eight bacteriological samples were collected from the dams and 145 from their 42 puppies. Colostrum/milk samples (n = 12) showed a bacterial growth mainly limited to few colonies. Staphylococci, Enterococci, E. coli, Proteus spp. were most frequently isolated. All vaginal swabs (n = 12) resulted in bacteria isolation (medium to high growth). Streptococci, Enterococci, E. coli were the most frequently detected. E. coli, Proteus mirabilis, Enterococcus spp., Streptococcus spp. were often obtained from dams’ and puppies’ rectal swabs. Clostridia, not isolated in any other sampling site, were rarely found (n = 3) in meconium while they were more frequently isolated at later times (T2: n = 30; T30: n = 17; T60: n = 27).

Analysis of the bacterial genus pattern over time showed a statistically significant reduction (P < 0.01) in the heterogeneity of microbial composition in all time points if compared to birth for each dam-litter unit. These results were confirmed with cluster analysis and two-dimensional scaling.

Conclusion

This novel data analysis suggests a fundamental role of the individual dam in seeding and shaping the microbiome of the litter. Thus, modulating the dam’s microbiota may positively impact the puppy microbiota and benefit their health.

The Species-Level Composition of the Fecal Bifidobacterium and Lactobacillus Genera in Indonesian Children Differs from That of Their Mothers

The infant gut microbiota plays a critical role in early life growth and derives mainly from maternal gut and breast milk. This study aimed to analyze the differences in the gut microbiota, namely Bifidobacterium and Lactobacillus communities at species level among breast milk as well as maternal and infant feces at different time points after delivery. Fifty-one mother–infant pairs from Indonesia were recruited, and the breast milk and maternal and infant feces were collected and analyzed by high throughput sequencing (16S rRNA, Bifidobacterium groEL and Lactobacillus groEL genes). PCoA results showed bacterial composition was different among breast milk and maternal and infant feces within the first two years. The abundance of Bifidobacterium and Bacteroides were significantly higher in infant feces compared to their maternal feces from birth to two years of age, and maternal breast milk within six months after birth (p < 0.05), whereas the abundance of Blautia, Prevotella, and Faecalibacterium was higher in maternal feces compared to that in breast milk within six months and infant feces within one year after birth, respectively (p < 0.05). The relative abundances of Bacteroides and Lactobacillus was higher and lower in infant feces compared to that in maternal feces only between one and two years of age, respectively (p < 0.05). For Bifidobacterium community at species level, B. adolescentis, B. ruminantium, B. longum subsp. infantis, B. bifidum, and B. pseudolongum were identified in all samples. However, the profile of Bifidobacterium was different between maternal and infant feces at different ages. The relative abundances of B. adolescentis and B. ruminantium were higher in maternal feces compared to those in infant feces from birth to one year of age (p < 0.05), while the relative abundances of B. longum subsp. infantis and B. bifidum were higher in infant feces compared to those in maternal feces beyond three months, and the relative abundance of B. pseudolongum was only higher in infant feces between three and six months (p < 0.05). For Lactobacillus community, L. paragasseri showed higher relative abundance in infant feces when the infant was younger than one year of age (p < 0.05). This study showed bacterial composition at the genus level and Bifidobacterium and Lactobacillus communities at the species level were stage specific in maternal breast milk as well as and maternal and infant feces.

Effects of Lactococcus lactis on the Intestinal Functions in Weaning Piglets

Post-weaning diarrhea of piglets is associated with gut microbiota dysbiosis and intestinal pathogen infection. Recent studies have shown that Lactococcus lactis (L.lactis) could help suppress pathogen infection. This study aimed to investigate the effects of L.lactis on various factors related to growth and immunity in weaning piglets. The results showed that L.lactis improved the growth performance, regulated the amino acid profile (for example, increasing serum tryptophan and ileal mucosal cystine) and the intestinal GABAergic system (including inhibiting ileal gene expression of SLC6A13, GABAAρ1, π, θ, and γ1, and promoting ileal GABAAα5 expression). L.lactis also modulated intestinal immunity by promoting jejunal interleukin 17, 18, 22, ileal toll-like receptor 2, 5, 6, and myeloid differentiation primary response protein 88 gene expression while inhibiting jejunal interferon-γ and ileal interleukin 22 expressions. L.lactis highly affected the intestinal microbiota by improving the beta diversity of gut microbiota and the relative abundance of Halomonas and Shewanella. In conclusion, L.lactis improved the growth performance and regulated amino acid profiles, intestinal immunity and microbiota in weaning piglets.

Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective

Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA R2=0.005, pseudo-F=2.643, P=0.001). A sparse partial least squares - discriminant analysis model trained using the gut microbiota of individuals from China, India and Indonesia (representation of Chinese, Indian and Malay ethnic group, respectively) showed a better-than-random performance in classifying Malaysian of Chinese descent, although the performance for Indian and Malay were modest (true prediction rate, Chinese=0.60, Indian=0.49, Malay=0.44). Separately, differential abundance analysis singled out Ligilactobacillus as being elevated in Indians. We postulate that despite the strong influence of geographical factors on the gut microbiota, cultural similarity due to a shared ethnic origin drives the presence of a shared gut microbiota composition. The interplay of these factors will likely depend on the circumstances of particular groups of migrants.

Gut Microbiome of a Multiethnic Community Possessed No Predominant Microbiota

With increasing globalisation, various diets from around the world are readily available in global cities. This study aimed to verify if multiethnic dietary habits destabilised the gut microbiome in response to frequent changes, leading to readily colonisation of exogenous microbes. This may have health implications. We profiled Singapore young adults of different ethnicities for dietary habits, faecal type, gut microbiome and cytokine levels. Subjects were challenged with Lactobacillus casei, and corresponding changes in microbiome and cytokines were evaluated. Here, we found that the majority of young adults had normal stool types (73% Bristol Scale Types 3 and 4) and faecal microbiome categorised into three clusters, irrespective of race and gender. Cluster 1 was dominated by Bacteroides, Cluster 2 by Prevotella, while Cluster 3 showed a marginal increase in Blautia, Ruminococaceae and Ruminococcus, without a predominant microbiota. These youngsters in the three faecal microbiome clusters preferred Western high sugary beverages, Southeast Asian plant-rich diet and Asian/Western diets in rotation, respectively. Multiethnic dietary habits (Cluster 3) led to a gut microbiome without predominant microbiota yet demonstrated colonisation resistance to Lactobacillus. Although Bacteroides and Prevotella are reported to be health-promoting but also risk factors for some illnesses, Singapore-style dietary rotation habits may alleviate Bacteroides and Prevotella associated ill effects. Different immunological outcome was observed during consumption of the lactobacilli among the three microbiome clusters.

Developmental Patterns of Fecal Bile Acids in Healthy Neonates and Children

Background

Normal profiles of FBAs in healthy neonates and children in Kunming city and surrounding areas in China have not been previously determined. The objective of this study was to determine a developmental pattern of fecal bile acids (FBAs) in healthy neonates and children.

Material/Methods

A cross-sectional study was performed on 238 healthy neonates and children recruited in the First Affiliated Hospital of Kunming Medical University, China from October 2015 to September 2016. Secreted primary and secondary FBAs in fresh feces were quantitated by liquid chromatography mass spectrometry (LC-MS). Amounts of FBAs in feces were compared among various age groups.

Results

Trace amounts of cholic acid and chenodiol acid of primary FBAs were detectable at day 3 after birth, with a significant increase from day 3 to day 7. The primary FBAs gradually decreased from day 25 to the age of 6 years old. In contrast, a significant amount of glycochenodeoxycholic acid was detected on day 3 but decreased to a trace amount by day 7 and onwards. Primary FBAs appeared to maintain a high level, accounting for 98% of total FBAs, with no significant changes from day 7 to day 25 after birth. They gradually decreased from 90% to 10% from age 6 months to 6 years old. While the secondary FBAs were barely detected in neonates, only accounting for 2% of total FBAs, they were gradually elevated to 90% of total FBAs from age 6 months to 6 years old.

Conclusions

The liver can effectively synthesize primary bile acids 7 days after birth, and fecal primary bile acids tend to be stable after the neonate stage. Secondary bile acids continuously increase along with the maturation of intestinal flora, which reaches a relatively stable level at around 3 years old.

Gut Microbiota and Short-Chain Fatty Acid Profile between Normal and Moderate Malnutrition Children in Yogyakarta, Indonesia

Malnutrition has been associated with the gut microbiota composition and the gastrointestinal environment. This study aimed to evaluate whether there is a difference in the gut microbiota profile between the normal and undernutrition (considered moderate malnutrition) children and evaluate the gastrointestinal environment observed from the short-chain fatty acid (SCFA) profile. Ten days' observations were done between normal (n:13) and undernutrition (n:15) children. The subject's diet was recorded using a food record. Analysis of the gut microbiota was performed using 16S rRNA gene sequencing targeting the V3-V4 variables region, while the SCFA profile was analyzed using gas chromatography. The result shows that the undernutrition group's energy intake was lower than in the normal group. Although there was no difference in diversity index and overall gut composition, overexpression of the genera Methanobrevibacter, Anaerococcus, Eubacterium, and Succinivibrio was observed in the undernutrition group. Meanwhile, in the normal group, Ruminococcus and Fusobacterium were found. In both groups, there was also the dominant of Prevotella enterotype. Gastrointestinal conditions in the normal group tended to be more acidic compared to the undernutrition group. It occurs due to the high concentration of propionate and butyric acids.

Gut microbiota and aging

Aging is characterized by the functional decline of tissues and organs and increased risk of aging-associated disorders, which pose major societal challenges and are a public health priority. Despite extensive human genetics studies, limited progress has been made linking genetics with aging. There is a growing realization that the altered assembly, structure and dynamics of the gut microbiota actively participate in the aging process. Age-related microbial dysbiosis is involved in reshaping immune responses during aging, which manifest as immunosenescence (insufficiency) and inflammaging (over-reaction) that accompany many age-associated enteric and extraenteric diseases. The gut microbiota can be regulated, suggesting a potential target for aging interventions. This review summarizes recent findings on the physiological succession of gut microbiota across the life-cycle, the roles and mechanisms of gut microbiota in healthy aging, alterations of gut microbiota and aging-associated diseases, and the gut microbiota-targeted anti-aging strategies.