The Maternal Milk Microbiome in Mammals of Different Types and Its Potential Role in the Neonatal Gut Microbiota Composition

Maternal milk, a main source of nutrition for neonates in early life, has attracted attention. An increasing number of studies have found that maternal milk has a high microbial diversity, as well as factors that might influence this diversity. However, there is a lack of knowledge regarding the effects of host diet and phylogeny on maternal milk microbes and the contribution of the maternal milk microbiota to the neonatal gut microbiota. Here, we analyzed the maternal milk and fecal microbiota of nine species (lion, dog, panda, human, mouse, rhesus macaque, cow, goat, and rabbit) of mammals of three type groups (herbivore, omnivore, and carnivore) using 16S rRNA amplicon sequencing. Our study provided evidence of host diet and phylogeny on the maternal milk microbiota. Moreover, functional prediction revealed that the carnivores had a significantly higher percentage of base excision repair, glycerolipid metabolism, taurine and hypotaurine metabolism, inorganic ion transport and metabolism, and nucleotide metabolism; while arginine and proline metabolism showed enrichment in the herbivore group. Source-tracking analysis showed that the contributions of bacteria from maternal milk to the microbiota of neonates of different mammals were different at day 3 after neonatal birth. Overall, our findings provided a theoretical basis for the maternal milk microbiota to affect neonatal fecal microbiota at day 3 after neonatal birth.

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Relationships between Gut Microbiota, Metabolome, Body Weight, and Glucose Homeostasis of Obese Dogs Fed with Diets Differing in Prebiotic and Protein Content

Microorganisms ◽

10.3390/microorganisms8040513 ◽

2020 ◽

Vol 8 (4) ◽

pp. 513 ◽

Cited By ~ 2

Author(s):

Emmanuelle Apper ◽

Lisa Privet ◽

Bernard Taminiau ◽

Cindy Le Bourgot ◽

Ljubica Svilar ◽

...

Keyword(s):

Gut Microbiota ◽

Glucose Homeostasis ◽

Energy Homeostasis ◽

Latin Square ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Protein Levels ◽

16S Rrna Amplicon Sequencing ◽

Metabolic Dysfunctions ◽

Nutritional Strategies

Obesity is a major issue in pets and nutritional strategies need to be developed, like promoting greater protein and fiber intake. This study aimed to evaluate the effects of dietary protein levels and prebiotic supplementation on the glucose metabolism and relationships between the gut, microbiota, metabolome, and phenotype of obese dogs. Six obese Beagle dogs received a diet containing 25.6% or 36.9% crude protein, with or without 1% short-chain fructo-oligosaccharide (scFOS) or oligofructose (OF), in a Latin-square study design. Fecal and blood samples were collected for metabolite analysis, untargeted metabolomics, and 16S rRNA amplicon sequencing. A multi-block analysis was performed to build a correlation network to identify relationships between fecal microbiota, metabolome, and phenotypic variables. Diets did not affect energy homeostasis, but scFOS supplementation modulated fecal microbiota composition and induced significant changes of the fecal metabolome. Bile acids and several amino acids were related to glucose homeostasis while specific bacteria gathered in metavariables had a high number of links with phenotypic and metabolomic parameters. It also suggested that fecal aminoadipate and hippurate act as potential markers of glucose homeostasis. This preliminary study provides new insights into the relationships between the gut microbiota, the metabolome, and several phenotypic markers involved in obesity and associated metabolic dysfunctions.

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Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests

Microbiome ◽

10.1186/s40168-020-00896-9 ◽

2020 ◽

Vol 8 (1) ◽

Author(s):

Cheng-Yu Chen ◽

Chih-Kuan Chen ◽

Yi-Ying Chen ◽

Andrew Fang ◽

Grace Tzun-Wen Shaw ◽

...

Keyword(s):

Gut Microbiota ◽

Zebra Finch ◽

Brood Parasitism ◽

Foster Parents ◽

Early Stage ◽

Amplicon Sequencing ◽

Oral Feeding ◽

Source Tracking ◽

Zebra Finches ◽

16S Rrna Amplicon Sequencing

Abstract Background Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments. Results Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them. Moreover, source-tracking models revealed high contribution of zebra finches’ oral cavity/crop microbiota to their chicks’ early gut microbiota, which were largely replaced by the parental gut microbiota at later stages. The results suggest that oral feeding only affects the early stage of hatchling gut microbial development. Conclusions Our study indicates that passerine chicks mainly acquire symbionts through indirect maternal transmission—passive environmental uptake from nests that were smeared with the intestinal and cloacal microbes of parents that raised them. Gut microbial diversity was low in hand-reared chicks, emphasizing the importance of parental care in shaping the gut microbiota. In addition, several probiotics were found in chicks fostered by society finches, which are excellent foster parents for other finches in bird farms and hosts of brood parasitism by zebra finches in aviaries; this finding implies that avian species that can transfer probiotics to chicks may become selectively preferred hosts of brood parasitism in nature.

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Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota

10.1101/313577 ◽

2018 ◽

Cited By ~ 1

Author(s):

Wei Yan ◽

Jiangxia Zheng ◽

Chaoliang Wen ◽

Congliang Ji ◽

Dexiang Zhang ◽

...

Keyword(s):

Small Intestine ◽

Community Structure ◽

Microbial Community ◽

Gut Microbiota ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Fecal Samples ◽

Community Membership ◽

16S Rrna Amplicon Sequencing ◽

Fecal Sampling

AbstractBackgroundDespite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum and feces samples, for 16S rRNA amplicon sequencing analyses.ResultsIn this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11 – 87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54 – 0.71 and 0.71 – 0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the 4 gut segments, and these correlations were not high (ρ = −0.2 – 0.4, P < 0.05) for most genera.ConclusionsOur results provide evidence that the good potential of feces to identify most taxa in chicken guts, but it should be interpreted with caution by using feces as a proxy for gut in microbial structure analyses. This work provides insights and future directions regarding the usage of fecal samples in studies of the gut microbiome.

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

Microorganisms ◽

10.3390/microorganisms9061237 ◽

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.

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H. pylori Eradication Treatment Alters Gut Microbiota and GLP-1 Secretion in Humans

Journal of Clinical Medicine ◽

10.3390/jcm8040451 ◽

2019 ◽

Vol 8 (4) ◽

pp. 451 ◽

Cited By ~ 11

Author(s):

Isabel Cornejo-Pareja ◽

Gracia Martín-Núñez ◽

M. Roca-Rodríguez ◽

Fernando Cardona ◽

Leticia Coin-Aragüez ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Carbohydrate Metabolism ◽

Eradication Therapy ◽

Amplicon Sequencing ◽

Antibiotic Use ◽

Metabolic Disturbances ◽

Bifidobacterium Adolescentis ◽

16S Rrna Amplicon Sequencing ◽

H Pylori

Changes in the intestinal microbial community and some metabolic disturbances, including obesity and type2 diabetes, are related. Glucagon-like peptide-1 (GLP-1) regulates glucose homeostasis. Microbiota have been linked to incretin secretion. Antibiotic use causes changes in microbial diversity and composition. Our aim was to evaluate the relationship between microbiota changes and GLP-1 secretion. A prospective case-control study with a Helicobacter pylori-positive patient model involving subjects under eradication therapy (omeprazole, clarithromycin, and amoxicillin). Forty patients with H. pylori infection and 20 matched participants, but negative for H. pylori antigen. Patients were evaluated before and two months after treatment. We analyzed anthropometric measurements, carbohydrate metabolism, lipid profile, and C-reactive protein. Gut microbiota composition was analyzed through 16S rRNA amplicon sequencing (IlluminaMiSeq). Eradication treatment for H. pylori decreased bacterial richness (Chao1, p = 0.041). Changes in gut microbiota profiles were observed at phylum, family, genus and species levels. GLP-1 secretion and variables of carbohydrate metabolism were improved. Correlations were seen between GLP-1 changes and variations within microbial community abundances, specifically Bifidobacterium adolescentis, the Lachnobacterium genus, and Coriobacteriaceae family. A conventional treatment to eradicate H. pylori could improve carbohydrate metabolism possibly in relation with an increase in GLP-1 secretion. GLP-1 secretion may be related to alterations in intestinal microbiota, specifically Lachnobacterium, B. adolescentis and Coriobacteriaceae.

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Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽

10.3390/genes10100748 ◽

2019 ◽

Vol 10 (10) ◽

pp. 748 ◽

Cited By ~ 5

Author(s):

Jin-Young Lee ◽

Mohamed Mannaa ◽

Yunkyung Kim ◽

Jehun Kim ◽

Geun-Tae Kim ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbiota Composition ◽

Stool Samples ◽

Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

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The Effect of Lactobacillus plantarum BW2013 on The Gut Microbiota in Mice Analyzed by 16S rRNA Amplicon Sequencing

Polish Journal of Microbiology ◽

10.33073/pjm-2021-022 ◽

2021 ◽

Vol 70 (2) ◽

pp. 235-243

Author(s):

TONG TONG ◽

XIAOHUI NIU ◽

QIAN LI ◽

YUXI LING ◽

ZUMING LI ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Dose Group ◽

Low Dose ◽

Amplicon Sequencing ◽

Control Group ◽

High Dose ◽

Treatment Groups ◽

16S Rrna Amplicon Sequencing ◽

Medium Dose

Lactobacillus plantarum BW2013 was isolated from the fermented Chinese cabbage. This study aimed to test the effect of this strain on the gut microbiota in BALB/c mice by 16S rRNA amplicon sequencing. The mice were randomly allocated to the control group and three treatment groups of L. plantarum BW2013 (a low-dose group of 108 CFU/ml, a medium-dose group of 109 CFU/ml, and a high-dose group of 1010 CFU/ml). The weight of mice was recorded once a week, and the fecal samples were collected for 16S rRNA amplicon sequencing after 28 days of continuous treatment. Compared with the control group, the body weight gain in the treatment groups was not significant. The 16S rRNA amplicon sequencing analysis showed that both the Chao1 and ACE indexes increased slightly in the medium-dose group compared to the control group, but the difference was not significant. Based on PCoA results, there was no significant difference in β diversity between the treatment groups. Compared to the control group, the abundance of Bacteroidetes increased in the low-dose group. The abundance of Firmicutes increased in the medium-dose group. At the genus level, the abundance of Alloprevotella increased in the low-dose group compared to the control group. The increased abundance of Ruminococcaceae and decreased abundance of Candidatus_Saccharimonas was observed in the medium-dose group. Additionally, the abundance of Bacteroides increased, and Alistipes and Candidatus_Saccharimonas decreased in the high-dose group. These results indicated that L. plantarum BW2013 could ameliorate gut microbiota composition, but its effects vary with the dose.

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Metformin induces weight loss associated with gut microbiota alteration in non-diabetic obese women: a randomized double-blind clinical trial

Acta Endocrinologica ◽

10.1530/eje-18-0826 ◽

2019 ◽

Vol 180 (3) ◽

pp. 165-176 ◽

Cited By ~ 14

Author(s):

Hanieh-Sadat Ejtahed ◽

Raul Y Tito ◽

Seyed-Davar Siadat ◽

Shirin Hasani-Ranjbar ◽

Zahra Hoseini-Tavassol ◽

...

Keyword(s):

Clinical Trial ◽

Gut Microbiota ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Pharmacological Therapy ◽

Microbiota Composition ◽

Obese Women ◽

Double Blind ◽

Baseline Values ◽

Gut Microbiota Composition

Objective The increasing prevalence of obesity over the past few decades constitutes a global health challenge. Pharmacological therapy is recommended to accompany life-style modification for obesity management. Here, we perform a clinical trial to investigate the effects of metformin on anthropometric indices and gut microbiota composition in non-diabetic, treatment-naive obese women with a low-calorie diet (LCD). Design Randomized double-blind parallel-group clinical trial Methods Forty-six obese women were randomly assigned to the metformin (500 mg/tab) or placebo groups using computer-generated random numbers. Subjects in both groups took two tablets per day for 2 months. Anthropometric measurements and collection of blood and fecal samples were done at the baseline and at the end of the trial. Gut microbiota composition was assessed using 16S rRNA amplicon sequencing. Results Twenty-four and twenty-two subjects were included in the metformin + LCD and placebo + LCD groups, respectively; at the end of trial, 20 and 16 subjects were analyzed. The metformin + LCD and placebo + LCD caused a 4.5 and 2.6% decrease in BMI from the baseline values, respectively (P < 0.01). Insulin concentration decreased in the metformin + LCD group (P = 0.046). The overall fecal microbiota composition and diversity were unaffected in the metformin + LCD group. However, a significant specific increase in Escherichia/Shigella abundance was observed after metformin + LCD intervention (P = 0.026). Fecal acetate concentration, but not producers, was significantly higher in the placebo + LCD group, adjusted for baseline values and BMI (P = 0.002). Conclusions Despite the weight reduction after metformin intake, the overall fecal microbiota composition remained largely unchanged in obese women, with exception of changes in specific proteobacterial groups.

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Korean Traditional Medicine (Jakyakgamcho-tang) Ameliorates Colitis by Regulating Gut Microbiota

Metabolites ◽

10.3390/metabo9100226 ◽

2019 ◽

Vol 9 (10) ◽

pp. 226 ◽

Cited By ~ 1

Author(s):

Seung-Ho Seo ◽

Tatsuya Unno ◽

Seong-Eun Park ◽

Eun-Ju Kim ◽

Yu-Mi Lee ◽

...

Keyword(s):

Gut Microbiota ◽

Amplicon Sequencing ◽

Control Group ◽

Scaling Analysis ◽

Aminosalicylic Acid ◽

Operational Taxonomic Units ◽

16S Rrna Amplicon Sequencing ◽

Cytokine Levels ◽

Korean Traditional Medicine ◽

Gut Microbial Community

The objective of this study was to examine the anti-colitis activity of Jakyakgamcho-tang (JGT) in dextran sulfate sodium (DSS)-induced colitis and explore changes of the gut microbial community using 16S rRNA amplicon sequencing and metabolomics approaches. It was found that treatment with JGT or 5-aminosalicylic acid (5-ASA) alleviated the severity of colitis symptoms by suppressing inflammatory cytokine levels of IL-6, IL-12, and IFN-γ. The non-metric multidimensional scaling analysis of gut microbiome revealed that JGT groups were clearly separated from the DSS group, suggesting that JGT administration altered gut microbiota. The operational taxonomic units (OTUs) that were decreased by DSS but increased by JGT include Akkermansia and Allobaculum. On the other hand, OTUs that were increased by DSS but decreased by 5-ASA or JGT treatments include Bacteroidales S24-7, Ruminococcaceae, and Rikenellaceae, and the genera Bacteroides, Parabacteroides, Oscillospira, and Coprobacillus. After JGT administration, the metabolites, including most amino acids and lactic acid that were altered by colitis induction, became similar to those of the control group. This study demonstrates that JGT might have potential to effectively treat colitis by restoring dysbiosis of gut microbiota and host metabolites.

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