scholarly journals Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

2021 ◽  
Author(s):  
Alice Baniel ◽  
Lauren Petrullo ◽  
Arianne Mercer ◽  
Laurie Reitsema ◽  
Sierra Sams ◽  
...  
Keyword(s):  
Maternal Effects ◽  
Gut Microbiome ◽  
Early Life ◽  
Amplicon Sequencing ◽  
Microbial Colonization ◽  
Fecal Samples ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Gut Colonization ◽  
First Time

Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mother's milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more "milk-oriented" compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization

scholarly journals Successional stages in infant gut microbiota maturation

2021 ◽  
Author(s):  
Leen Beller ◽  
Ward Deboutte ◽  
Gwen Falony ◽  
Sara Vieira Silva ◽  
Raul Tito ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Early Life ◽  
Microbial Colonization ◽  
Maturation Stage ◽  
Gut Flora ◽  
Microbiome Composition ◽  
Gut Colonization ◽  
Maturation Stages ◽  
Colonization Process ◽  
First Year Of Life

Background: Disturbances in the primary colonization of the infant gut can result in life-long consequences and have been associated with a range of host conditions. Although early life factors have been shown to affect the infant gut microbiota development, our current understanding of the human gut colonization in early life remains limited. To gain more insights in the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (total number of samples, n=303). To evaluate gut microbiota maturation transition towards an adult configuration, we compared the microbiome composition of the infants to the Flemish Gut Flora Project population (n=1,106). Results: We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the Flemish Gut Flora Project (FGFP) cohort clustered all infant samples within the (in adults) potentially dysbiotic Bact2 enterotype. Conclusion: We confirmed similarities between infant gut microbial colonization and adult dysbiosis. A profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected.

scholarly journals Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome

2021 ◽  
Vol 12 ◽  
Author(s):  
Emma Diamond ◽  
Katharine Hewlett ◽  
Swathi Penumutchu ◽  
Alexei Belenky ◽  
Peter Belenky
Keyword(s):  
Gut Microbiome ◽  
Burkholderia Cepacia ◽  
Coffee Consumption ◽  
Amplicon Sequencing ◽  
Antibiotic Use ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Caffeinated Coffee

The microbiome is essential for host health, and perturbations resulting from antibiotic use can lead to dysbiosis and disease. Diet can be a powerful modulator of microbiome composition and function, with the potential to mitigate the negative effects of antibiotic use. Thus, it is necessary to study the impacts of diet and drug interactions on the gut microbiome. Coffee is a commonly consumed beverage containing many compounds that have the potential to affect the microbiome, including caffeine, polyphenols, and fiber. We supplemented mice with caffeinated and decaffeinated coffee in conjunction with amoxicillin, and used 16S rRNA amplicon sequencing of fecal samples to investigate changes in diversity and composition of the murine fecal microbiome. We found that antibiotics, regardless of coffee supplementation, caused significant disruption to the murine fecal microbiome, enriching for Proteobacteria, Verrucomicrobia, and Bacteroidetes, but reducing Firmicutes. While we found that coffee alone did not have a significant impact on the composition of the fecal microbiome, coffee supplementation did significantly affect relative abundance metrics in mice treated with amoxicillin. After caffeinated coffee supplementation, mice treated with amoxicillin showed a smaller increase in Proteobacteria, specifically of the family Burkholderiaceae. Correspondingly we found that in vitro, Burkholderia cepacia was highly resistant to amoxicillin, and that it was inhibited by concentrations of caffeine and caffeinated coffee comparable to levels of caffeine in murine ceca. Overall, this work shows that coffee, and possibly the caffeine component, can impact both the microbiome and microbiome members during antibiotic exposure.

scholarly journals Anopheles albimanus natural microbiota is altered within one generation of laboratory colonization

2020 ◽  
Author(s):  
Nsa Dada ◽  
Ana Cristina Benedict ◽  
Francisco López ◽  
Juan C. Lol ◽  
Mili Sheth ◽  
...  
Keyword(s):  
First Generation ◽  
Amplicon Sequencing ◽  
Anopheles Albimanus ◽  
Microbiome Composition ◽  
Laboratory Conditions ◽  
16S Rrna Amplicon Sequencing ◽  
Late Instar ◽  
Microbe Interactions ◽  
First Time ◽  
Natural Microbiota

AbstractResearch on mosquito-microbe interactions may lead to new tools for mosquito and mosquito-borne disease control. To date, such research has largely utilized laboratory-reared mosquitoes that typically lack the microbial diversity of wild populations. A logical progression in this area involves working under controlled settings using field-derived mosquitoes or, in most cases, their progeny. Thus, an understanding of how laboratory colonization affects the assemblage of mosquito microbiota would aid in advancing mosquito microbiome studies and their applications beyond laboratory settings. Using high throughput 16S rRNA amplicon sequencing, we characterized the internal and cuticle surface microbiota of F1 progeny of wild-caught adult Anopheles albimanus from four locations in Guatemala. A total of 132 late instar larvae and 135 2-5day old, non-blood-fed virgin adult females that were reared under identical laboratory conditions, were pooled (3 individuals/pool) and analyzed. F1 larvae from different maternal sites showed different microbial compositions (p=0.001; F = 9.5), but these differences were absent at the adult stage (p=0.12; F =1.6). These results suggest that field-acquired mosquito microbiota may be lost in as early as the first generation of colonization under normal laboratory conditions, thus, requiring adjustments to maintain field-derived microbiota. This is the first time that the microbiota of F1 progeny of wild-caught mosquitoes has been characterized in relation to maternal collection site. Our findings provide a comprehensive background for studying how parentage and environmental conditions differentially or concomitantly affect mosquito microbiome composition, and how this can be exploited in advancing mosquito microbiome studies and their applications beyond laboratory settings.

scholarly journals Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study

2021 ◽  
Vol 9 (6) ◽  
pp. 1237
Author(s):  
Han-Na Kim ◽  
Eun-Jeong Joo ◽  
Chil-Woo Lee ◽  
Kwang-Sung Ahn ◽  
Hyung-Lae Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gastrointestinal Symptoms ◽  
Amplicon Sequencing ◽  
Recovery Phase ◽  
Fecal Samples ◽  
Intestinal Microbes ◽  
Gut Dysbiosis ◽  
16S Rrna Amplicon Sequencing ◽  
Microbiome Data ◽  
Negative Conversion

Patients with COVID-19 have been reported to experience gastrointestinal symptoms as well as respiratory symptoms, but the effects of COVID-19 on the gut microbiota are poorly understood. We explored gut microbiome profiles associated with the respiratory infection of SARS-CoV-2 during the recovery phase in patients with asymptomatic or mild COVID-19. A longitudinal analysis was performed using the same patients to determine whether the gut microbiota changed after recovery from COVID-19. We applied 16S rRNA amplicon sequencing to analyze two paired fecal samples from 12 patients with asymptomatic or mild COVID-19. Fecal samples were selected at two time points: during SARS-CoV-2 infection (infected state) and after negative conversion of the viral RNA (recovered state). We also compared the microbiome data with those from 36 healthy controls. Microbial evenness of the recovered state was significantly increased compared with the infected state. SARS-CoV-2 infection induced the depletion of Bacteroidetes, while an abundance was observed with a tendency to rapidly reverse in the recovered state. The Firmicutes/Bacteroidetes ratio in the infected state was markedly higher than that in the recovered state. Gut dysbiosis was observed after infection even in patients with asymptomatic or mild COVID-19, while the composition of the gut microbiota was recovered after negative conversion of SARS-CoV-2 RNA. Modifying intestinal microbes in response to COVID-19 might be a useful therapeutic alternative.

scholarly journals Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

2019 ◽  
Vol 97 (11) ◽  
pp. 4567-4578 ◽  
Author(s):  
Margaret D Weinroth ◽  
Jennifer N Martin ◽  
Enrique Doster ◽  
Ifigenia Geornaras ◽  
Jennifer K Parker ◽  
...  
Keyword(s):  
Liver Abscess ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Feedlot Cattle ◽  
Microbiome Composition ◽  
Soil Microbial ◽  
16S Rrna Amplicon Sequencing ◽  
Liver Abscesses ◽  
Geographical Regions ◽  
Antimicrobial Resistance Genes

Abstract Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

scholarly journals An association between chronic widespread pain and the gut microbiome

Rheumatology ◽  
2020 ◽  
Author(s):  
Maxim B Freidin ◽  
Maria A Stalteri ◽  
Philippa M Wells ◽  
Genevieve Lachance ◽  
Andrei-Florin Baleanu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Chronic Widespread Pain ◽  
Mendelian Randomisation ◽  
Total N ◽  
16S Rrna Amplicon Sequencing ◽  
A Genome

Abstract Objectives Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP. Methods CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterised using 16S rRNA amplicon sequencing and amplicon sequence variants (ASVs), and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors. Results Alpha diversity was significantly lower in CWP cases than controls (Mann–Whitney test, p-values 2.3e-04 and 1.2e-02, respectively). The species Coprococcus comes was significantly depleted in CWP cases (p.adj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, p= 7.4e-8). A Mendelian randomisation study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP. Conclusions We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.

scholarly journals Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

mSphere ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Steven A. Frese ◽  
Andra A. Hutton ◽  
Lindsey N. Contreras ◽  
Claire A. Shaw ◽  
Michelle C. Palumbo ◽  
...  
Keyword(s):  
Human Milk ◽  
Gut Microbiome ◽  
Bifidobacterium Longum ◽  
Specific Substrate ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
Breastfed Infants ◽  
Gut Function ◽  
First Time

ABSTRACT The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function. Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32). Fecal samples were collected during the first 60 postnatal days in both groups. Fecal samples were assessed by 16S rRNA gene sequencing, quantitative PCR, mass spectrometry, and endotoxin measurement. B. infantis-fed infants had significantly higher populations of fecal Bifidobacteriaceae, in particular B. infantis, while EVC001 was fed, and this difference persisted more than 30 days after EVC001 supplementation ceased. Fecal milk oligosaccharides were significantly lower in B. infantis EVC001-fed infants, demonstrating higher consumption of human milk oligosaccharides by B. infantis EVC001. Concentrations of acetate and lactate were significantly higher and fecal pH was significantly lower in infants fed EVC001, demonstrating alterations in intestinal fermentation. Infants colonized by Bifidobacteriaceae at high levels had 4-fold-lower fecal endotoxin levels, consistent with observed lower levels of Gram-negative Proteobacteria and Bacteroidetes. IMPORTANCE The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function.

Formula Supplementation of the Breastfed Infant: Assault on the Gut Microbiome

2014 ◽  
Vol 5 (4) ◽  
pp. 128-132 ◽  
Author(s):  
Marsha Walker
Keyword(s):  
Breast Milk ◽  
Health Outcomes ◽  
Milk Production ◽  
Gut Microbiome ◽  
Side Effect ◽  
Early Life ◽  
Microbial Colonization ◽  
Mucosal Inflammation ◽  
Maternal Milk ◽  
Allergic Disorders

Although formula supplementation is well known to have detrimental effects on the duration and exclusivity of breastfeeding, on the maternal milk production, and on the health outcomes of mothers and infants, there are immediate and long-lasting effects on the infant’s gut microbiome. Breast milk is an important element modulating the metabolic and immunological programming relative to a child’s health. An unfavorable or abnormal microbial colonization during early life interferes with many functions in the gut and facilitates invasion of pathogens and foreign or harmful antigens. Alterations of the gut environment (such as from supplementation with formula) are directly responsible for mucosal inflammation and disease, autoimmunity conditions, and allergic disorders in childhood and adulthood. Clinicians and parents will benefit from knowledge of this side effect of formula supplementation.

scholarly journals Preterm Birth Is Correlated With Increased Oral Originated Microbiome in the Gut

2021 ◽  
Vol 11 ◽  
Author(s):  
Chunhua Yin ◽  
Jingrui Chen ◽  
Xuena Wu ◽  
Yeling Liu ◽  
Quan He ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Gut Microbiome ◽  
Preterm Labor ◽  
Amplicon Sequencing ◽  
Oral Bacteria ◽  
Gut Bacteria ◽  
Oral Microbiome ◽  
16S Rrna Amplicon Sequencing ◽  
Threatened Preterm Labor ◽  
Adverse Pregnancy

BackgroundPreterm birth is one of the leading causes of perinatal morbidity and mortality. Gut microbiome dysbiosis is closely related to adverse pregnancy outcomes. However, the role of the gut microbiome in the pathogenesis of preterm birth remains poorly studied.MethodWe collected fecal samples from 41 women (cases presenting with threatened preterm labor =19, 11 of which delivered preterm; gestational age-matched no-labor controls, all of which delivered at term = 22) were recruited for the study. We performed 16S rRNA amplicon sequencing to compare the composition of the gut microbiome in threatened preterm labor cases and controls and among women who delivered preterm and at term. By annotating taxonomic biomarkers with the Human Oral Microbiome Database, we observed an increased abundance of potential oral-to-gut bacteria in preterm patients.ResultsPatients with preterm birth showed a distinct gut microbiome dysbiosis compared with those who delivered at term. Opportunistic pathogens, particularly Porphyromonas, Streptococcus, Fusobacterium, and Veillonella, were enriched, whereas Coprococcus and Gemmiger were markedly depleted in the preterm group. Most of the enriched bacteria were annotated oral bacteria using the Human Oral Microbiome Database. These potential oral-to-gut bacteria were correlated with clinical parameters that reflected maternal and fetal status.ConclusionsThis study suggests that patients who deliver preterm demonstrate altered gut microbiome that may contain higher common oral bacteria.

scholarly journals Delivery mode impacts newborn gut colonization efficiency

2020 ◽  
Author(s):  
Caroline Mitchell ◽  
Larson Hogstrom ◽  
Allison Bryant ◽  
Agnes Bergerat ◽  
Avital Cher ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Dominant Factor ◽  
Delivery Mode ◽  
Metagenomic Sequencing ◽  
Vaginal Microbiome ◽  
Abdominal Incision ◽  
Birth Canal ◽  
Microbiome Composition ◽  
Gut Colonization ◽  
Infant Gut Microbiome

AbstractDelivery mode is the variable with the greatest influence on the infant gut microbiome composition in the first few months of life. Children born by Cesarean section (C-section) lack species from the Bacteroides genus in their gut microbial community, and this difference can be detectable until 6-18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome, as children born by C-section do not pass through the birth canal; however, Bacteroides species are not common members of the vaginal microbiome, thus this explanation seems inadequate. Here, we set out to re-evaluate this hypothesis by collecting rectal and vaginal samples before delivery from 73 mothers with paired stool from their infants in the first two weeks of life. We compared microbial profiles of infants born by planned, pre-labor C-section to those born by emergent, post-labor surgery (where the child was in the birth canal, but eventually delivered through an abdominal incision), and found no significant differences in the microbiome between these two groups. Both groups showed the characteristic signature lack of Bacteroides species, despite their difference in exposure to the birth canal. Surprisingly, this signature was only evident in samples from week two of life, but not in the first week. Children born by C-section often had high abundance of Bacteroides in their first few days of life, but these were not stable colonizers of the infant gut, as they were not detectable by week two. Finally, we used metagenomic sequencing to compare microbial strains in maternal vaginal and rectal samples and samples from their infants; we found evidence for mother-to-child transmission of rectal rather than vaginal strains. These results challenge birth canal exposure as the dominant factor in infant gut microbiome establishment and implicate colonization efficiency rather than exposure as a dictating factor of the newborn gut microbiome composition.

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