Dietary Supplementation with Goji Berries (Lycium barbarum) Modulates the Microbiota of Digestive Tract and Caecal Metabolites in Rabbits

Goji berries show health benefits, although the possible mechanisms of action, including compositional changes in the gut microbiome, are still not fully understood. The aim of this study was to evaluate the effect of Goji berry supplementation on microbiota composition and metabolites in the digestive tracts of rabbits. Twenty-eight New Zealand White rabbits were fed with a commercial feed (control group, C; n = 14) or the same diet supplemented with 3% of Goji berries (Goji group, G; n = 14), from weaning (35 days old) until slaughter (90 days old). At slaughter, samples from the content of the gastrointestinal tracts were collected and analyzed by Next Generation 16S rRNA Gene Sequencing to evaluate the microbial composition. Ammonia and lactic acid were also quantified in caecum. Results showed differences in microbiota composition between the groups for two phyla (Cyanobacteria and Euryarchaeota), two classes (Methanobacteria and Bacilli), five orders, fourteen families, and forty-five genera. Ruminococcaceae (p < 0.05) and Lachnospiraceae (p < 0.01) were more abundant in G than in C group. Lactobacillaceae also showed differences between the two groups, with Lactobacillus as the predominant genus (p = 0.002). Finally, Goji berry supplementation stimulated lactic acid fermentation (p < 0.05). Thus, Goji berry supplementation could modulate gastrointestinal microbiota composition and caecal fermentation.

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Ultrafine particles altered gut microbial population and metabolic profiles in a sex-specific manner in an obese mouse model

Scientific Reports ◽

10.1038/s41598-021-85784-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kundi Yang ◽

Mengyang Xu ◽

Jingyi Cao ◽

Qi Zhu ◽

Monica Rahman ◽

...

Keyword(s):

Ultrafine Particles ◽

Microbial Population ◽

Phosphate Buffer Solution ◽

Biodiesel Fuel ◽

Control Group ◽

Obese Mouse ◽

Rrna Gene ◽

Obese Mice ◽

Microbial Composition ◽

Increased Risk

AbstractEmerging evidence has highlighted the connection between exposure to air pollution and the increased risk of obesity, metabolic syndrome, and comorbidities. Given the recent interest in studying the effects of ultrafine particle (UFP) on the health of obese individuals, this study examined the effects of gastrointestinal UFP exposure on gut microbial composition and metabolic function using an in vivo murine model of obesity in both sexes. UFPs generated from light-duty diesel engine combustion of petrodiesel (B0) and a petrodiesel/biodiesel fuel blend (80:20 v/v, B20) were administered orally. Multi-omics approaches, including liquid chromatography–mass spectrometry (LC–MS) based targeted metabolomics and 16S rRNA gene sequence analysis, semi-quantitatively compared the effects of 10-day UFP exposures on obese C57B6 mouse gut microbial population, changes in diversity and community function compared to a phosphate buffer solution (PBS) control group. Our results show that sex-specific differences in the gut microbial population in response to UFP exposure can be observed, as UFPs appear to have a differential impact on several bacterial families in males and females. Meanwhile, the alteration of seventy-five metabolites from the gut microbial metabolome varied significantly (ANOVA p < 0.05) across the PBS control, B0, and B20 groups. Multivariate analyses revealed that the fuel-type specific disruption to the microbial metabolome was observed in both sexes, with stronger disruptive effects found in females in comparison to male obese mice. Metabolic signatures of bacterial cellular oxidative stress, such as the decreased concentration of nucleotides and lipids and increased concentrations of carbohydrate, energy, and vitamin metabolites were detected. Furthermore, blood metabolites from the obese mice were differentially affected by the fuel types used to generate the UFPs (B0 vs. B20).

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Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats

10.1101/2021.05.28.446115 ◽

2021 ◽

Author(s):

Evangelia Stavroulaki ◽

Jan S. Suchodolski ◽

Rachel Pilla ◽

Geoffrey T. Fosgate ◽

Chi-Hsuan Sung ◽

...

Keyword(s):

Clavulanic Acid ◽

Antibiotic Treatment ◽

Control Group ◽

Rrna Gene ◽

Upper Respiratory Tract ◽

Long Term Effects ◽

Microbial Composition ◽

Increased Risk ◽

Group 15 ◽

Amoxicillin Clavulanic Acid

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.

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The microbiota of farmed mink (Neovison vison) follows a successional development and is affected by early life antibiotic exposure

Scientific Reports ◽

10.1038/s41598-020-77417-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Martin Iain Bahl ◽

Anabelle Legarth Honoré ◽

Sanne Tygesen Skønager ◽

Oliver Legarth Honoré ◽

Tove Clausen ◽

...

Keyword(s):

Gut Microbiota ◽

Early Life ◽

Intramuscular Administration ◽

Control Group ◽

Rrna Gene ◽

Antibiotic Administration ◽

Lactation Period ◽

Microbiota Composition ◽

Gut Microbiota Composition ◽

Successional Development

AbstractOn many mink farms, antibiotics are used extensively during the lactation period to reduce the prevalence and severity of pre-weaning diarrhoea (PWD) in mink kits (also referred to as greasy kit syndrome). Concerns have been raised, that routine treatment of PWD with antibiotics could affect the natural successional development of the gut microbiota, which may have long lasting consequences. Here we investigated the effects of early life antibiotic treatment administered for 1 week (postnatal days 13–20). Two routes of antibiotic administration were compared to a non-treated control group (CTR, n = 24). Routes of administration included indirect treatment, through the milk from dams receiving antibiotics by intramuscular administration (ABX_D, n = 24) and direct treatment by intramuscular administration to the kits (ABX_K, n = 24). A tendency for slightly increased weight at termination (Day 205) was observed in the ABX_K group. The gut microbiota composition was profiled by 16S rRNA gene sequencing at eight time points between Day 7 and Day 205. A clear successional development of the gut microbiota composition was observed and both treatment regimens caused detectable changes in the gut microbiota until at least eight days after treatment ceased. At termination, a significant positive correlation was identified between microbial diversity and animal weight.

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The urinary microbiota composition remains stable over time and under various storage conditions

10.1101/2019.12.13.875187 ◽

2019 ◽

Cited By ~ 1

Author(s):

Caspar Bundgaard-Nielsen ◽

Nadia Ammitzbøll ◽

Yusuf Abdi Isse ◽

Abdisalam Muqtar ◽

Ann-Maria Jensen ◽

...

Keyword(s):

Urinary Tract ◽

Study Design ◽

Storage Conditions ◽

Rrna Gene ◽

Microbiota Composition ◽

Microbial Composition ◽

Male Adult ◽

Bacterial Composition ◽

Urinary Microbiota ◽

Over Time

AbstractBackgroundNew sensitive techniques have revealed a large population of bacteria in the human urinary tract, challenging the perception of the urine of healthy humans being sterile. While the role of this urinary microbiota is unknown, dysbiosis has been linked to disorders like urgency urinary incontinence and interstitial cystitis. When comparing studies it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether storage condition or time of collection, had any impact on the urinary microbial composition.ResultsFor comparison of different storage conditions, urine was collected from five healthy adult female donors, and analyzed by 16S rRNA gene sequencing. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in nineteen healthy donors, including four women, five men, five girls, and five boys. With the exception of two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of the urinary microbiota was found to be highly resilient to changes introduced by storage temperature and duration. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys.Together our study supports flexibility in study design, when conducting urinary microbiota studies.Author summaryThe discovery of bacteria native to the urinary tract in healthy people, a location previously believed to be sterile, has prompted research into the clinical potential of these bacteria. However, methodological weaknesses can significantly influence such studies, and thus development of robust techniques for investigating these bacteria are needed. In the present study, we investigated whether differences in storage following collection, could affect the bacterial composition of urine samples. Next, we investigated if this composition exhibited daily or day-to-day variations.Firstly, we found, that the bacterial composition of urine could be maintained by storage at −80 °C, −20 °C, or refrigerated at 4 °C. Secondly, the bacterial composition of urine remained stable over time. Overall, the results of this study provide information important to study design in future investigations into the clinical implications of urinary bacteria.

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Gut microbiota composition does not associate with Toxoplasma infection in rats

10.22541/au.163898245.55631982/v1 ◽

2021 ◽

Author(s):

Patrick Taggart ◽

Craig Liddicoat ◽

Wen Han Tong ◽

Martin Breed ◽

Philip Weinstein ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Chronic Phase ◽

Negative Control ◽

Control Group ◽

Rrna Gene ◽

Gastrointestinal Microbiota ◽

Toxoplasma Infection ◽

Behavioural Changes

Toxoplasma infection in intermediate host species closely associates with inflammation. This association has led to suggestions that the behavioural changes associated with infection may be indirectly driven by the resulting sustained inflammation rather than a direct behavioural manipulation by the parasite. If this is correct, sustained inflammation in chronically infected rodents should present as widespread changes in the gastrointestinal microbiota due to the dependency between the composition of these microbiota and sustained inflammation. We conducted a randomized controlled experiment in rats that were assigned to a Toxoplasma-treatment, placebo-treatment or negative control group. We sacrificed rats during the chronic phase of infection, collected their cecal stool samples and sequenced the V3-V4 region of the 16S rRNA gene to characterise the bacterial community in these samples. Toxoplasma infection did not induce widespread changes in the bacterial community composition of the gastrointestinal tract of rats. Rather, we found sex differences in the bacterial community composition and only minor changes in Toxoplasma infected rats. We conclude that it is unlikely that sustained inflammation is the mechanism driving the highly specific behavioural changes observed in Toxoplasma-positive rats.

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Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions

Nutrients ◽

10.3390/nu11020467 ◽

2019 ◽

Vol 11 (2) ◽

pp. 467 ◽

Cited By ~ 8

Author(s):

Yanbei Wu ◽

Robert Li ◽

Haiqiu Huang ◽

Arnetta Fletcher ◽

Lu Yu ◽

...

Keyword(s):

Prostate Cancer ◽

Tumor Growth ◽

Gut Microbiome ◽

Species Interactions ◽

Tumor Development ◽

Xenograft Model ◽

Microbial Interactions ◽

Control Group ◽

Rrna Gene ◽

Microbial Composition

Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks. The effects of dietary I3C on gut microbial composition and microbial species interactions were then examined by 16s rRNA gene-based sequencing and co-occurrence network analysis. I3C supplementation significantly inhibited tumor growth (p < 0.0001) and altered the structure of gut microbiome. The abundance of the phylum Deferribacteres, more specifically, Mucispirillum schaedleri, was significantly increased by dietary I3C. Additionally, I3C consumption also changed gut microbial co-occurrence patterns. One of the network modules in the control group, consisting of seven bacteria in family S-27, was positively correlated with tumor size (p < 0.009). Moreover, dietary I3C disrupted microbial interactions and altered this association between specific microbial network and tumor development. Our results unraveled complex relationships among I3C ingestion, gut microbiota, and prostate tumor development and may provide a novel insight into the mechanism for the chemopreventive effect of dietary I3C on prostate cancer.

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Animal Rennets as Sources of Dairy Lactic Acid Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.03837-13 ◽

2014 ◽

Vol 80 (7) ◽

pp. 2050-2061 ◽

Cited By ~ 25

Author(s):

Margherita Cruciata ◽

Ciro Sannino ◽

Danilo Ercolini ◽

Maria L. Scatassa ◽

Francesca De Filippis ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

16S Rrna ◽

16S Rrna Gene ◽

Streptococcus Thermophilus ◽

Species Level ◽

Lactobacillus Delbrueckii ◽

Rrna Gene ◽

Microbial Composition ◽

Content Type

ABSTRACTThe microbial composition of artisan and industrial animal rennet pastes was studied by using both culture-dependent and -independent approaches. Pyrosequencing targeting the 16S rRNA gene allowed to identify 361 operational taxonomic units (OTUs) to the genus/species level. Among lactic acid bacteria (LAB),Streptococcus thermophilusand some lactobacilli, mainlyLactobacillus crispatusandLactobacillus reuteri, were the most abundant species, with differences among the samples. Twelve groups of microorganisms were targeted by viable plate counts revealing a dominance of mesophilic cocci. All rennets were able to acidify ultrahigh-temperature-processed (UHT) milk as shown by pH and total titratable acidity (TTA). Presumptive LAB isolated at the highest dilutions of acidified milks were phenotypically characterized, grouped, differentiated at the strain level by randomly amplified polymorphic DNA (RAPD)-PCR analysis, and subjected to 16S rRNA gene sequencing. Only 18 strains were clearly identified at the species level, asEnterococcus casseliflavus,Enterococcus faecium,Enterococcus faecalis,Enterococcus lactis,Lactobacillus delbrueckii, andStreptococcus thermophilus, while the other strains, all belonging to the genusEnterococcus, could not be allotted into any previously described species. The phylogenetic analysis showed that these strains might represent different unknown species. All strains were evaluated for their dairy technological performances. All isolates produced diacetyl, and 10 of them produced a rapid pH drop in milk, but only 3 isolates were also autolytic. This work showed that animal rennet pastes can be sources of LAB, mainly enterococci, that might contribute to the microbial diversity associated with dairy productions.

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Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (Lagopus muta japonica) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria

Microorganisms ◽

10.3390/microorganisms6030077 ◽

2018 ◽

Vol 6 (3) ◽

pp. 77 ◽

Cited By ~ 5

Author(s):

Atsushi Ueda ◽

Atsushi Kobayashi ◽

Sayaka Tsuchida ◽

Takuji Yamada ◽

Koichi Murata ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Captive Breeding ◽

Wild Animals ◽

Microbial Structure ◽

Gastrointestinal Microbiota ◽

Microbial Composition ◽

Conservation Program ◽

Lagopus Muta ◽

High Level

Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of Japanese mountains, and the dominant cecal microbial structure of wild Japanese rock ptarmigans is elucidated. Coriobacteraceae and Lachnospraceae were the two dominant bacterial families in all samples analyzed. At the genus level, 10 genera Olsenella, Actinomyces, Megasphaera, Slackia, Cloacibacillus, Bifidobacterium,Escherichia,Dialister, Megamonas, and Bilophila were dominant. These results reveal the high level of coexistence of lactic acid bacteria (Olsenella and Bifidobacterium) and lactate-utilizing bacteria (Megasphaera). This coexistence should be taken into account for the successful breeding of captive Japanese rock ptarmigans in the national conservation program.

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Dietary trans-10, cis-12-conjugated linoleic acid alters fatty acid metabolism and microbiota composition in mice

British Journal Of Nutrition ◽

10.1017/s0007114514004206 ◽

2015 ◽

Vol 113 (5) ◽

pp. 728-738 ◽

Cited By ~ 50

Author(s):

Tatiana M. Marques ◽

Rebecca Wall ◽

Orla O'Sullivan ◽

Gerald F. Fitzgerald ◽

Fergus Shanahan ◽

...

Keyword(s):

Lipid Metabolism ◽

Linoleic Acid ◽

Gut Microbiota ◽

Conjugated Linoleic Acid ◽

Control Group ◽

Standard Diet ◽

Microbiota Composition ◽

Microbial Composition ◽

16S Rrna Pyrosequencing ◽

Gut Microbiota Composition

The main aim of the present study was to investigate the effects of dietary trans-10, cis-12-conjugated linoleic acid (t10c12-CLA) on intestinal microbiota composition and SCFA production. C57BL/6 mice (n 8 per group) were fed a standard diet either supplemented with t10c12-CLA (0·5 %, w/w) (intervention) or with no supplementation (control), daily for 8 weeks. Metabolic markers (serum glucose, leptin, insulin and TAG, and liver TAG) were assessed by ELISA commercial kits, tissue long-chain fatty acids and caecal SCFA by GC, and microbial composition by 16S rRNA pyrosequencing. Dietary t10c12-CLA significantly decreased visceral fat mass (P< 0·001), but did not affect body weight (intervention), when compared with no supplementation (control). Additionally, lipid mass and composition were affected by t10c12-CLA intake. Caecal acetate, propionate and isobutyrate concentrations were higher (P< 0·05) in the t10c12-CLA-supplemented group than in the control group. The analysis of the microbiota composition following 8 weeks of t10c12-CLA supplementation revealed lower proportions of Firmicutes (P= 0·003) and higher proportions of Bacteroidetes (P= 0·027) compared with no supplementation. Furthermore, t10c12-CLA supplementation for 8 weeks significantly altered the gut microbiota composition, harbouring higher proportions of Bacteroidetes, including Porphyromonadaceae bacteria previously linked with negative effects on lipid metabolism and induction of hepatic steatosis. These results indicate that the mechanism of dietary t10c12-CLA on lipid metabolism in mice may be, at least, partially mediated by alterations in gut microbiota composition and functionality.

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Sugar Beet Pectin Supplementation Did Not Alter Profiles of Fecal Microbiota and Exhaled Breath in Healthy Young Adults and Healthy Elderly

Nutrients ◽

10.3390/nu11092193 ◽

2019 ◽

Vol 11 (9) ◽

pp. 2193 ◽

Cited By ~ 4

Author(s):

Ran An ◽

Ellen Wilms ◽

Agnieszka Smolinska ◽

Gerben D.A. Hermes ◽

Ad A.M. Masclee ◽

...

Keyword(s):

Young Adults ◽

Sugar Beet ◽

Healthy Aging ◽

Fecal Microbiota ◽

Rrna Gene ◽

Exhaled Breath ◽

Microbiota Composition ◽

Microbial Composition ◽

Double Blind ◽

Healthy Elderly

Aging is accompanied with increased frailty and comorbidities, which is potentially associated with microbiome perturbations. Dietary fibers could contribute to healthy aging by beneficially impacting gut microbiota and metabolite profiles. We aimed to compare young adults with elderly and investigate the effect of pectin supplementation on fecal microbiota composition, short chain fatty acids (SCFAs), and exhaled volatile organic compounds (VOCs) while using a randomized, double-blind, placebo-controlled parallel design. Fifty-two young adults and 48 elderly consumed 15 g/day sugar beet pectin or maltodextrin for four weeks. Fecal and exhaled breath samples were collected before and after the intervention period. Fecal samples were used for microbiota profiling by 16S rRNA gene amplicon sequencing, and for analysis of SCFAs by gas chromatography (GC). Breath was used for VOC analysis by GC-tof-MS. Young adults and elderly showed similar fecal SCFA and exhaled VOC profiles. Additionally, fecal microbiota profiles were similar, with five genera significantly different in relative abundance. Pectin supplementation did not significantly alter fecal microbiota, SCFA or exhaled VOC profiles in elderly or young adults. In conclusion, aside from some minor differences in microbial composition, healthy elderly and young adults showed comparable fecal microbiota composition and activity, which were not altered by pectin supplementation.

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