scholarly journals Selective maternal seeding and rearing environment from birth to weaning shape the developing piglet gut microbiome

2020 ◽  
Author(s):  
Chen Wei ◽  
Jiandui Mi ◽  
Jingyun Ma ◽  
Yiming Jiang ◽  
Li Deng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Primary Source ◽  
Vaginal Microbiota ◽  
Source Tracking ◽  
Gut Health ◽  
Community Patterns ◽  
Relative Contribution ◽  
Microbial Sources ◽  
Over Time

Abstract Background: The acquisition and development of the mammalian microbiome early in life are critical to establish a healthy host-microbiome symbiosis. The maternal and environmental microbial reservoirs are considered the main sources of microbial communities in newborn mammals. However, the timely relative contribution of various microbial sources to the colonization of the gut microbiota in newborn piglets remains unclear. The aim of this study was to investigate the influence of the sow and delivery environment microbes on nursing piglets from birth through weaning.Results: We longitudinally sampled the microbiota of 20 sow-piglet pairs (three piglets per sow) from multiple body sites and the surrounding weaning environment from birth to 28 days postpartum (1,119 samples in total) reared under identical conditions. Source-tracking analysis revealed that the contribution of various microbial sources to the piglet gut microbiome gradually changed over time. The neonatal microbiota was initially sparsely populated and predominantly comprised taxa from the maternal vaginal microbiota that increased gradually from 69.0% at day 0 to 89.3% at day 3 and dropped to 0.28% at day 28. As the piglets aged, the major microbiota community patterns were most strongly associated with the sow feces and slatted floor, with contributions increasing from 0.52% and 9.6% at day 0 to 62.1% and 33.8% at day 28, respectively. The intestinal microbial diversity, composition and function significantly changed as the piglets aged, and 30 age-discriminatory bacterial taxa were identified with distinctive time-dependent shifts in their relative abundance, which likely reflected the effect of the maternal and environmental microbial sources on the selection and adaptation of the piglet gut microbiota.Conclusions: Vaginal microbiota is the primary source of the gut microbiota in piglets within three days after birth and are gradually replaced by the sow fecal and slatted floor microbiota over time. These finding may offer novel strategies to promote the establishment of exogenous symbiotic microbes to improve piglet gut health.

scholarly journals Impact of whole grains on the gut microbiota: the next frontier for oats?

2014 ◽  
Vol 112 (S2) ◽  
pp. S44-S49 ◽  
Author(s):  
Devin J. Rose
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Gut Microbiome ◽  
Resistant Starch ◽  
Health Benefits ◽  
Whole Grains ◽  
Gut Health ◽  
Gut Function ◽  
Complex Lipids

The gut microbiota plays important roles in proper gut function and can contribute to or help prevent disease. Whole grains, including oats, constitute important sources of nutrients for the gut microbiota and contribute to a healthy gut microbiome. In particular, whole grains provide NSP and resistant starch, unsaturated TAG and complex lipids, and phenolics. The composition of these constituents is unique in oats compared with other whole grains. Therefore, oats may contribute distinctive effects on gut health relative to other grains. Studies designed to determine these effects may uncover new human-health benefits of oat consumption.

scholarly journals Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiome in wild and farmed large yellow croaker

2021 ◽  
Author(s):  
Jun Zhu ◽  
Hao Li ◽  
Ze-Zhou Jing ◽  
Wei Zheng ◽  
Yuan-Rong Luo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Learning Algorithm ◽  
High Ratio ◽  
Source Tracking ◽  
Large Yellow Croaker ◽  
Diet Change ◽  
Wild Stock ◽  
Key Factor ◽  
Stochastic Assembly

Abstract BackgroundRevealing the potential divergence of gut microbiome between farmed and wild fishes, and its underlying mechanism are informative to improve its mariculture, as well as establish the molecular marker of host source tracking, which is an alternative to the yet-to-be-established host genetic marker. A candidate for testing the feasibility is the large yellow croaker, Larimichthys crocea , which is carnivorous and ranking the top maricultural fish in China with depleted wild resource and frequently farmed individuals escaping and fry releasing for wild stock enhancement. ResultsThe rectums of wild (n=212) and farmed (n=79) individuals from multiple batches were collected for the profiling of gut bacterial communities. The farmed individuals had a higher alpha diversity and lower bacterial loading than the wild individuals. The gut microbiota of the two sources exhibited divergence and high inter-batch variation, featured by the dominance of Psychrobacter spp. in the wild group. Predicted function of gut microbiome and representative isolates suggested that diet could be a key factor for the divergence, which was linked to the high ratio and diverse source of carbohydrate in formulated feed and low pH of rectum contents in farmed fishes. The non-stochastic distribution patterns of the core gut microbiota of the wild and farmed individuals indicated the feasibility of microbiota-based host source tracking through machine learning algorithm. Random forest classifier building on the divergence and non-stochastic assembly of gut microbiome was robust in host source tracking for individuals from all batches including a newly introduced batch. ConclusionsOur study revealed the divergence of the gut microbiota between wild and farmed croakers and suggested that diet change is an underlying key factor for the divergence. As the first time, we verified that with less biased datasets and non-stochastic pattern, gut microbiota can be robustly applied to the tracking of host source even in carnivorous fish.

scholarly journals Probiotics maintain the gut microbiome homeostasis during Indian Antarctic expedition by ship

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ashish Kumar Srivastava ◽  
Vishwajeet Rohil ◽  
Brij Bhushan ◽  
Malleswara Rao Eslavath ◽  
Harshita Gupta ◽  
...  
Keyword(s):  
Placebo Group ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Glycoside Hydrolases ◽  
Gut Health ◽  
Microbial Composition ◽  
Carbohydrate Binding Modules ◽  
Antarctic Expedition ◽  
Probiotic Intervention ◽  
The Impact

AbstractShip voyage to Antarctica is a stressful journey for expedition members. The response of human gut microbiota to ship voyage and a feasible approach to maintain gut health, is still unexplored. The present findings describe a 24-day long longitudinal study involving 19 members from 38th Indian Antarctic Expedition, to investigate the impact of ship voyage and effect of probiotic intervention on gut microbiota. Fecal samples collected on day 0 as baseline and at the end of ship voyage (day 24), were analyzed using whole genome shotgun sequencing. Probiotic intervention reduced the sea sickness by 10% compared to 44% in placebo group. The gut microbiome in placebo group members on day 0 and day 24, indicated significant alteration compared to a marginal change in the microbial composition in probiotic group. Functional analysis revealed significant alterations in carbohydrate and amino acid metabolism. Carbohydrate-active enzymes analysis represented functional genes involved in glycoside hydrolases, glycosyltransferases and carbohydrate binding modules, for maintaining gut microbiome homeostasis. Suggesting thereby the possible mechanism of probiotic in stabilizing and restoring gut microflora during stressful ship journey. The present study is first of its kind, providing a feasible approach for protecting gut health during Antarctic expedition involving ship voyage.

The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and is Influenced by Medication Exposures, Age, Environment, and Frailty

2021 ◽  
Author(s):  
John P Haran ◽  
Abigail Zeamer ◽  
Doyle V Ward ◽  
Protiva Dutta ◽  
Vanni Bucci ◽  
...  
Keyword(s):  
Older Adults ◽  
Gut Microbiota ◽  
Older Adult ◽  
Gut Microbiome ◽  
Assessment Tool ◽  
Mini Nutritional Assessment ◽  
Metagenomic Sequencing ◽  
Mixed Effect ◽  
Stool Samples ◽  
Over Time

Abstract Older adults in nursing homes (NHs) have increased frailty, medication, and antimicrobial exposures, all factors that are known to affect the composition of gut microbiota. Our objective was to define which factors have the greatest association with the NH resident gut microbiota, explore patterns of dysbiosis and compositional changes in gut microbiota over time in this environment. We collected serial stool samples from NH residents. Residents were assessed using the Mini Nutritional Assessment tool and Clinical Frailty Scale. Bacterial composition of resident stool samples was determined by metagenomic sequencing. We used mixed-effect random forest modeling to identify clinical covariates that associate with microbiota. We enrolled and followed 166 residents from 5 NHs collecting 512 stool samples and following 15 residents for > 1 year. Medications, particularly psychoactive and anti-hypertensive medications, had the greatest effect on the microbiota. Age and frailty also contributed, and were associated with increased and decreased diversity, respectively. The microbiota of residents who had lived in the NH for > 1 year were enriched in inflammatory and pathogenic species and reduced in anti-inflammatory and symbiotic species. We observed intra-individual stability of the microbiome among older adults who had lived in the NH already for >1 year followed with sample collections 1 year apart. Older adult NH gut microbiome is heavily influenced by medications, age, and frailty. This microbiome is influenced by length of NH residence with dysbiosis becoming evident at 12 months, however after this point there is demonstrated relative stability over time.

scholarly journals Functional enrichment of gut microbiome by early supplementation of Bacillus based probiotic in cage free hens: a field study

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Samiullah Khan ◽  
Kapil K. Chousalkar
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Egg Production ◽  
Rna Degradation ◽  
Functional Enrichment ◽  
Internal Quality ◽  
Gut Health ◽  
Probiotic Supplementation ◽  
Cationic Antimicrobial Peptide ◽  
Significant Difference

Abstract Background The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. However, there is limited information on the interaction of Bacillus based probiotics with gut microbial community members in cage free laying chickens both in rearing and production phases of life. In the current study, we investigated the changes in the gut microbiome of free range hens in the field after Bacillus based probiotic supplementation. Results Overall, at phylum level, probiotic supplementation increased the populations of Bacteroidetes and Proteobacteria mainly at the expense of Firmicutes. The population of Bacteroidetes significantly increased during the production as compared to the rearing phase, and its higher population in the probiotic-supplemented chickens reflects the positive role of Bacillus based probiotic in gut health. Core differences in the beta diversity suggest that probiotic supplementation decreased microbial compositionality. The non-significant difference in alpha diversity between the probiotic and control chickens showed that the composition of community structure did not change. No Salmonella spp. were isolated from the probiotic supplemented birds. Egg internal quality was significantly higher, while egg production and body weight did not differ. Functional prediction data showed that probiotic supplementation enriched metabolic pathways, such as vitamin B6 metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis, RNA degradation, retinol metabolism, pantothenate and CoA biosynthesis, phosphonate and phosphinate metabolism, AMPK signaling pathway, cationic antimicrobial peptide (CAMP) resistance and tyrosine metabolism. Conclusions Overall, age was the main factor affecting the composition and diversity of gut microbiota, where probiotic supplementation improved the abundance of many useful candidates in the gut microbial communities. The generated baseline data in the current study highlights the importance of the continuous use of Bacillus based probiotic for optimum gut health and production.

scholarly journals Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

2012 ◽  
Vol 78 (17) ◽  
pp. 6153-6160 ◽  
Author(s):  
Elizabeth A. Maga ◽  
Prerak T. Desai ◽  
Bart C. Weimer ◽  
Nguyet Dao ◽  
Dietmar Kültz ◽  
...  
Keyword(s):  
Human Milk ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Gut Health ◽  
Content Type ◽  
Microbiome Composition ◽  
The Impact ◽  
Over Time

ABSTRACTHuman milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels ofFirmicutes(Clostridia) declined whereas those ofBacteroidetesincreased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P< 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (BifidobacteriaceaeandLactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae,Streptococcaceae,Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

scholarly journals Dietary Filamentous Fungi and Duration of Feeding Modulates Gut Microbial Composition in Rainbow Trout (Oncorhynchus mykiss)

2021 ◽  
Vol 8 ◽  
Author(s):  
Aprajita Singh ◽  
Sajjad Karimi ◽  
Aleksandar Vidakovic ◽  
Johan Dicksved ◽  
Markus Langeland ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Gut Microbiota ◽  
Filamentous Fungi ◽  
Gut Microbiome ◽  
Feeding Trial ◽  
Microbial Composition ◽  
Feed Processing ◽  
Commercial Diet ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Over Time

Changes in gut microbial composition over time in rainbow trout fed differentially processed diets supplemented with the filamentous fungi Neurospora intermedia were investigated in a 30-day feeding trial. Fish were fed a reference diet, non-preconditioned diet (NPD), or preconditioned (heat-treated) diet (PD), with the same inclusion level of N. intermedia in diets NPD and PD. Gut microbiota were analyzed on day 0, 10, 20, and 30. Gut microbial composition was similar for all diets on day 0, but was significantly different at day 10 and day 20. On day 30, the gut again contained similar communities irrespective of diet. The overall gut microbiota for each diet changed over time. Abundance of Peptostreptococcus and Streptococcus was higher in the initial days of feeding in fish fed on commercial diet, while a significant increase in lactic acid bacteria (Lactococcus lactis) was observed on day 30. Feed processing (preconditioning) did not contribute largely in shaping the gut microbiome. These results indicate that dietary manipulation and duration of feeding should be considered when evaluating gut microbial composition in cultured fish. A minimum 30-day feeding trial is suggested for gut microbiome, host and diet interaction studies.

scholarly journals Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Wenjun Liu ◽  
Jiachao Zhang ◽  
Chunyan Wu ◽  
Shunfeng Cai ◽  
Weiqiang Huang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Dietary Habits ◽  
Cerebrovascular Diseases ◽  
Living Environment ◽  
Intestinal Microbiome ◽  
High Morbidity ◽  
Metagenomic Sequencing ◽  
Gut Health ◽  
Taxonomic Profile

Abstract The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian’s gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment.

scholarly journals Sustained Drug Treatment Alters the Gut Microbiota in Rheumatoid Arthritis

2021 ◽  
Vol 12 ◽  
Author(s):  
Liyan Mei ◽  
Zhihua Yang ◽  
Xiaolin Zhang ◽  
Zehao Liu ◽  
Maojie Wang ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Drug Treatment ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Causative Role ◽  
Clinical Indicators ◽  
Reactive Protein ◽  
Over Time

Several studies have investigated the causative role of the microbiome in the development of rheumatoid arthritis (RA), but changes in the gut microbiome in RA patients during drug treatment have been less well studied. Here, we tracked the longitudinal changes in gut bacteria in 22 RA patients who were randomized into two groups and treated with Huayu-Qiangshen-Tongbi formula (HQT) plus methotrexate (MTX) or leflunomide (LEF) plus MTX. There were differences in the gut microbiome between untreated (at baseline) RA patients and healthy controls, with 37 species being more abundant in the RA patients and 21 species (including Clostridium celatum) being less abundant. Regarding the functional analysis, vitamin K2 biosynthesis was associated with RA-enriched bacteria. Additionally, in RA patients, alterations in gut microbial species appeared to be associated with RA-related clinical indicators through changing various gut microbiome functional pathways. The clinical efficacy of the two treatments was further observed to be similar, but the response trends of RA-related clinical indices in the two treatment groups differed. For example, HQT treatment affected the erythrocyte sedimentation rate (ESR), while LEF treatment affected the C-reactive protein (CRP) level. Further, 11 species and 9 metabolic pathways significantly changed over time in the HQT group (including C. celatum, which increased), while only 4 species and 2 metabolic pathways significantly changed over time in the LEF group. In summary, we studied the alterations in the gut microbiome of RA patients being treated with HQT or LEF. The results provide useful information on the role of the gut microbiota in the pathogenesis of RA, and they also provide potentially effective directions for developing new RA treatments.

scholarly journals Effect of Environmental Exposures on the Gut Microbiota from Early Infancy to Two Years of Age

2021 ◽  
Vol 9 (10) ◽  
pp. 2140
Author(s):  
Kameron Y. Sugino ◽  
Tengfei Ma ◽  
Nigel Paneth ◽  
Sarah S. Comstock
Keyword(s):  
Gut Microbiota ◽  
Human Milk ◽  
Gut Microbiome ◽  
Linear Models ◽  
Antibiotic Use ◽  
Temporal Variations ◽  
Milk Intake ◽  
Microbiome Composition ◽  
Infant Gut Microbiome ◽  
Over Time

The gut microbiota undergoes rapid changes during infancy in response to early-life exposures. We have investigated how the infant gut bacterial community matures over time and how exposures such as human milk and antibiotic treatment alter gut microbiota development. We used the LonGP program to create predictive models to determine the contribution of exposures on infant gut bacterial abundances from one month to two years of age. These models indicate that infant antibiotic use, human milk intake, maternal pre-pregnancy BMI, and sample shipping time were associated with changes in gut microbiome composition. In most infants, Bacteroides, Lachnospiraceae unclassified, Faecalibacterium, Akkermansia, and Phascolarctobacterium abundance increased rapidly after 6 months, while Escherichia, Bifidobacterium, Veillonella, and Streptococcus decreased in abundance over time. Individual, time-varying, random effects explained most of the variation in the LonGP models. Multivariate association with linear models (MaAsLin) displayed partial agreement with LonGP in the predicted trajectories over time and in relation to significant factors such as human milk intake. Multiple factors influence the dynamic changes in bacterial composition of the infant gut. Within-individual differences dominate the temporal variations in the infant gut microbiome, suggesting individual temporal variability is an important feature to consider in studies with a longitudinal sampling design.

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