Establishment Of Gut Microbiome Research Articles

The microbiome is dispensable for normal respiratory function and chemoreflexes in mice.

Increasing evidence indicates an association between microbiome composition and respiratory homeostasis and disease, particularly disordered breathing, such as obstructive sleep apnea. Previous work showing respiratory disruption is limited by the methodology employed to disrupt, eliminate, or remove the microbiome by antibiotic depletion. Our work utilized germ-free mice born without a microbiome and described respiratory alterations. We used whole-body flow through barometric plethysmography to assay conscious and unrestrained C57BL/6J germ-free (GF, n = 24) and specific-pathogen-free (SPF, n = 28) adult mice (with an intact microbiome) in normoxic (21% O2,79% N2) conditions and during challenges in hypercapnic (5% CO2, 21% O2, 74% N2) and hypoxic (10% O2, 90% N2) environments. Following initial plethysmography analysis, we performed fecal transplants to test the ability of gut microbiome establishment to rescue any observed phenotypes. Data were comprehensively analyzed using our newly published respiratory analysis software, Breathe Easy, to identify alterations in respiratory parameters, including ventilatory frequency, tidal volume, ventilation, apnea frequency, and sigh frequency. We also considered possible metabolic changes by analyzing oxygen consumption, carbon dioxide production, and ventilatory equivalents of oxygen. We also assayed GF and SPF neonates in an autoresuscitation assay to understand the effects of the microbiome on cardiorespiratory stressors in early development. We found several differences in baseline and recovery cardiorespiratory parameters in the neonates and differences in body weight at both ages studied. However, there was no difference in the overall survival of the neonates, and in contrast to prior studies utilizing gut microbial depletion, we found no consequential respiratory alterations in GF versus SPF adult mice at baseline or following fecal transplant in any groups. Interestingly, we did see alterations in oxygen consumption in the GF adult mice, which suggests an altered metabolic demand. Results from this study suggest that microbiome alteration in mice may not play as large a role in respiratory outcomes when a less severe methodology to eliminate the microbiome is utilized.

A39 DEVELOPMENTALLY REGULATED CECAL CONTENT MICRO-RNAS CORRELATE WITH MATURING MICROBIOTA GENES AND FUNCTIONS IN JUVENILE MICE

Abstract Background The gut microbiome establishment in early life is critical to life-long health and influenced by the maternal gut ecosystem. MicroRNAs (miRNAs) have emerged as a new player in host-microbiota interaction due to their regulatory effect on bacterial genes. We previously found that maternal supplementation with a probiotic mix of Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus R0052 supported the maturation of microbial metabolic activity and altered the cecal content miRNA profile in juvenile mice. Aims To investigate the relationship between cecal content miRNAs and inferred microbiota genes and functions in early life and identify potential miRNA-bacterial gene targets. Methods We generated 16S rRNA gene sequencing and NanoString nCounter® data from the cecal content of 14, 21, and 36-days-old C57BL/6 mice born to dams receiving or not probiotic-supplemented water since preconception. Taxa contributions to bacterial enzyme-encoding genes and pathways were inferred with PICRUSt2. Time or group-altered genes, pathways, and miRNAs were identified with DESeq2. Spearman correlations were performed between miRNAs and bacterial genes or pathways (n= 3-5 male offspring/PND/group) and significant correlations (q ampersand:003C 0.05) were visualized with NAViGaTOR. Potential miRNA binding sites on bacterial genes were investigated using the ViennaRNA Package. Results Time-associated miR-433 positively correlated with two time-altered genes involved in the TCA and glyoxylate cycles. Group-associated miR-691 was positively correlated with genes related to tRNA charging pathway, pyruvate fermentation to acetate and lactate, and amino acids biosynthesis. Additionally, miR-691 was negatively correlated with six group-altered genes involved in myo-inositol degradation. We identified potential miRNA binding sites (total free energy of binding ampersand:003C -10 kcal/mol) for miR-691 with genes involved in pyruvate fermentation, lysine biosynthesis, and myo-inositol degradation, and for miR-433 with genes annotated to the TCA and glyoxylate cycles. Conclusions Host miRNAs correlate with bacterial pathways and genes maturing during the weaning transition, highlighting their potential to regulate microbial metabolic activity. Maternal probiotics supplementation may accelerate the development of microbial metabolic pathways through epigenetic mechanisms, independently of weaning dietary shift. Correlations identified include energy production pathways and may become clinical targets in infants with delayed maturation of the intestinal ecosystem. Funding Agencies NSERC

Delivery mode and maternal gestational diabetes are important factors in shaping the neonatal initial gut microbiota.

The infant gut microbiome's establishment is pivotal for health and immune development. Understanding it unveils insights into growth, development, and maternal microbial interactions. Research often emphasizes gut bacteria, neglecting the phageome. To investigate the influence of geographic or maternal factors (mode of delivery, mode of breastfeeding, gestational diabetes mellitus) on the gut microbiota and phages of newborns, we collected fecal samples from 34 pairs of mothers and their infants within 24 hours of delivery from three regions (9 pairs from Enshi, 7 pairs from Hohhot, and 18 pairs from Hulunbuir) using sterile containers. Gut microbiota analysis by Shotgun sequencing was subsequently performed. Our results showed that geographic location affects maternal gut microbiology (P < 0.05), while the effect on infant gut microbiology was not significant (P = 0.184). Among the maternal factors, mode of delivery had a significant (P < 0.05) effect on the newborn. Specific bacteria (e.g., Bacteroides, Escherichia spp., Phocaeicola vulgatus, Escherichia coli, Staphylococcus hominis, Veillonella spp.), predicted active metabolites, and bacteriophage vOTUs varied with delivery mode. Phocaeicola vulgatus significantly correlated with some metabolites and bacteriophages in the early infant gut (P < 0.05). In the GD group, a strong negative correlation of phage diversity between mother and infants was observed (R = -0.58, P=0.04). In conclusion, neonatal early gut microbiome (including bacteria and bacteriophages) colonization is profoundly affected by the mode of delivery, and maternal gestational diabetes mellitus. The key bacteria may interact with bacteriophages to influence the levels of specific metabolites. Our study provides new evidence for the study of the infant microbiome, fills a gap in the analysis of the infant gut microbiota regarding the virome, and emphasizes the importance of maternal health for the infant initial gut virome.

Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species

The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2’-fucosyllactose (2’FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2’FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2’FL breakdown, thus critical for B. breve’s growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2’FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual’s microbiome.

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis.

The gut microbiome regulates various metabolic pathways in the host and its dysbiosis is involved in the pathogenesis of diverse diseases. One of the major factors triggering gut microbiome establishment is diet. This study aims to unravel interactions and changes between diet and gut microbiome over a period of 3 years. This study investigates the relation between diet and the microbiome of 75 individuals over a 3-year time period. Shotgun metagenomic sequencing is performed to profile gut microbial composition and function. This study shows that there are significant changes in gut microbiome taxonomy and functional composition between two time points. Whereas microbial taxonomy is found to be highly individualized, overall microbial functions stay relatively stable. Moreover, in silico metabolic modeling of microbial communities indicates that changes in dietary intake of medium-chain saturated fatty acids is accompanied by an altered utilization of amino acids by the gut microbiome. The study design allows us to validate functional stability within the gut microbiome of healthy subjects over a 3-year period. However, enduring changes in nutrition such as increased alcohol consumption or decreased intake of vegetables come along with enhanced microbial functions that are associated with disease etiology.

First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment.

The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon).

Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.

Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

BackgroundEarly development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management.ResultsGut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. DCM foal microbiomes were more similar to their dams in week five and six than were SFM foals at the same age.ConclusionsThis study demonstrates the impact of management on the development of the foal gut microbiome in the first 6 weeks of life. The higher numbers of taxa within and between bacterial groups found in SFM dams and foals suggests more diversity and functional redundancy in their gut microbiomes, which could lend greater stability and resiliency to these communities. The colonization of lactic acid bacteria in the early life of DCM foals suggests enrichment in response to the availability of dams’ feed. Thus, management type is an important driver of gut microbiome establishment on horses, and we may look to semi-feral horses for guidance in defining a healthy gut microbiome for domestic horses.

Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics.

Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.

Distribution of gut microbiome in infants with different delivery modes and feeding patterns

Objective To investigate the distribution characteristics of the gut microbiome in infants with different delivery mode and feeding pattern at six weeks of life. Methods A total of 60 infants delivered between June and September in 2017 at Peking University First Hospital were recruited. According to delivery modes and feeding patterns, they were respectively divided into two groups, which were vaginal delivery (n=42) and cesarean delivery (n=18) groups, and exclusively breastfeeding (n=40) and mixed-feeding (n=20) groups. Stool samples of all subjects were collected at six weeks after birth. The V3-V4 region of 16s rRNA gene was sequenced on Illumina Hiseq 2500 platform, and the results were analyzed with SILVA database and QIIME software. Independent samples t-test or Mann-Whitney U test was used for statistical analysis. Results (1) Eight bacterial phyla and 146 genera were identified in the 60 stool samples. Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were four dominant phyla, and Bifidobacterium, Clostridium, Klebsiella, Bacteroides, Streptococcus, Escherichia-Shigella, Veillonella and Faecalibacterium were the top eight most abundant genera. (2) At the phyla level, the vaginal delivery group was characterized with reduced Firmicutes (0.56±0.10 vs 0.42±0.20, t=2.94, P 0.05). At the genus level, the relative abundance of Bifidobacterium was higher in the vaginal delivery group than in the cesarean delivery group [0.19 (0.02-0.36) vs 0.01 (0.00-0.07), U=210, P 0.05). (3) The vaginal delivery group showed significantly lower Shannon and Simpson indexes than the cesarean delivery group [4.26 (3.61-5.52) vs 5.48±1.19, U=227, P 0.05). However, there was no significant difference in OTU number, Chao1, Shannon or Simpson index between the exclusively breastfeeding and the mixed-feeding groups (all P>0.05). Conclusion The early infancy is a critical period for the establishment of gut microbiome. Significant differences in the composition and diversity of gut microbiota are found between infants born vaginally and abdominally, but not in infants with different feeding patterns. Key words: Infant; Gastrointestinal microbiome; Delivery, obstetric; Feeding behavior