Trillions of microbes have evolved with and continue to live on human beings. With the rapid advances in tools and technology in recent years, new knowledge and insight in cross-talk between the microbes and their hosts have gained. It is the aim of this work to critically review and summarize recent literature reports on the role of microbiota and mechanisms involved in the progress and development of major human diseases, which include obesity, hypertension, cardiovascular disease, diabetes, cancer, Inflammatory Bowel Disease (IBD), gout, depression and arthritis, as well as infant health and longevity.

As an effective means to improve quality of life and prevent diseases, the demand for probiotics and related products has increased in recent years. However, it is still unclear whether a particular probiotic strain will have similar beneficial effects on healthy adults from different regions. In this study, the probiotic Lactobacillus casei Zhang (LCZ) was consumed by healthy adults from six different Asian regions and the changes in gut microbiota were compared using PacBio single molecule, real-time (SMRT) sequencing technology based on samples collected before, during and after consumption of LCZ. Our results reveal that the effect of LCZ consumption on individuals was closely related to the composition of that individual’s basal gut microbiota. A Gut Microbiota Variability Index (GMVI) was proposed to quantitatively compare the effects of LCZ on human gut microecology. Subjects from Xinjiang and Singapore regions had the highest and lowest GMVI, respectively. In general, consumption of LCZ increased the relative abundance of certain beneficial bacteria such as Lactobacillus, Roseburia, Coprococcus and Eubacterium rectale, while it inhibited growth of certain harmful bacteria such as Blautia and Ralstonia pickettii. In addition, consumption of LCZ was responsible for the conversion of some participants from Prevotella copri/Faecalibacterium prausnitzii (PF) enterotype to Faecalibacterium prausnitzii/Bacteroides dorei (FB) enterotype and consistently increased the abundance of lactic acid bacteria in the gut. It also increased/enhanced phosphate metabolic modules, amino acid transport systems, and isoleucine biosynthesis, but conversely decreased lipopolysaccharide biosynthesis. These changes could have health benefits for healthy adults.

Gastrointestinal (GI) microbiota play an important role in human health and wellbeing and the first wave of gut microbes arrives mostly through vertical transmission from mother to child. This study has undertaken to understand the microbiota profile of healthy Southeast Asian mother-infant pairs. Here, we examined the fecal, vaginal and breast milk microbiota of Indonesian mothers and the fecal microbiota of their children from less than 1 month to 48 months old. To determine the immune status of children and the effect of diet at different ages, we examined the level of cytokines, bile acids in the fecal water and weaning food frequency. The fecal microbiota of the children before weaning contained mainly Bacteroides and Bifidobacterium, which presented at low abundance in the samples of mothers. After weaning, the fecal microbiome of children was mainly of the Prevotella type, with decreasing levels of Bifidobacterium, thus becoming more like the fecal microbiome of the mother. The abundance of infant fecal commensals generally correlated inversely with potential pathogens before weaning. The fecal Bifidobacterium in children correlated inversely with the consumption of complex carbohydrates and fruits after weaning. The specific cytokines related to the proliferation and maturation of immunity were found to increase after weaning. A decreasing level of primary bile acids and an increase of secondary bile acids were observed after weaning. This study highlights the change in the GI microbiota of infants to adult-type microbiota after weaning and identifies diet as a major contributing factor.

Recent studies have realized the link between gut microbiota and human health and diseases. The question of diet, environment or gene is the determining factor for dominant microbiota and microbiota profile has not been fully resolved, for these comparative studies have been performed on populations of different ethnicities and in short-term intervention studies. Here, the Southern Chinese populations are compared, specifically the children of Guangzhou City (China), Penang City (west coast Malaysia) and Kelantan City (east coast Malaysia). These Chinese people have similar ancestry thus it would allow us to delineate the effect of diet and ethnicity on gut microbiota composition. For comparison, the Penang and Kelantan Malay children were also included. The results revealed that differences in microbiota genera within an ethnicity in different cities was due to differences in food type. Sharing the similar diet but different ethnicity in a city or different cities and living environment showed similar gut microbiota. The major gut microbiota (more than 1% total Operational Taxonomy Units, OTUs) of the children population are largely determined by diet but not ethnicity, environment, and lifestyle. Elucidating the link between diet and microbiota would facilitate the development of strategies to improve human health at a younger age.

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.

To validate survival of Lactobacillus casei strain Shirota (LcS) during passage through the gastrointestinal tract of healthy Singaporean young adults, 21 participants (18-25 years old) were asked to consume a 100 ml of fermented milk drink containing 1.0×10⁸ cfu/ml of LcS daily for 14 days, and to maintain their dietary habit and life style. During and at the end of the ingestion period, both culture method (identity confirmed by ELISA) and 16s rRNA sequencing results revealed that viable LcS (7.27 and 7.64 log₁₀ cfu/g of faeces at the ingestion period Day 7 and Day 14, respectively) and Lactobacillus could be recovered from the faeces of all the subjects. The viable LcS count from male and female were comparable for each time point. Before consumption (baseline) and 14 days after cessation of consumption of the fermented milk, LcS was not detected in most of the subjects. In this study condition, the composition of the major gut microbiota (>0.1% in relative abundance of genus) and characteristics of defaecation such as stool consistency and frequency of defecation did not change throughout the study before and after ingestion of LcS. LcS was able to survive passage through the gastrointestinal tract of Singapore adults without sustainable colonisation, but the effect of LcS on microbiota modulation, stool consistency and frequency was not observed under this study condition.