Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores

Abstract Background Through the rapid development in DNA sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal orders and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species including two carnivore suborders Canoidea and Feloidea as well as the orders of herbivore Perissodactyla and Artiodactyla held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3–V4 region of the 16S rRNA gene using Illumina MiSeq. Results We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of Carnivora is highly variable and inconsistent within and between species, Perissodactyla and Ruminantia show fewer differences across species boundaries. Furthermore, low-abundance bacterial families show higher fluctuations in the fecal microbiota than high-abundance ones. Conclusions Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of about 10 samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these within-species fluctuations balanced out in most cases and led to constant and more reliable results.

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Changes in the Fecal Microbiota Associated with a Broad-Spectrum Antimicrobial Administration in Hospitalized Neonatal Foals with Probiotics Supplementation

Animals ◽

10.3390/ani11082283 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2283

Author(s):

Francesca Freccero ◽

Aliai Lanci ◽

Jole Mariella ◽

Elisa Viciani ◽

Sara Quercia ◽

...

Keyword(s):

Broad Spectrum ◽

Alpha Diversity ◽

Illumina Miseq ◽

Fecal Microbiota ◽

Antimicrobial Treatment ◽

Rrna Gene ◽

The Mean ◽

Mean Time ◽

The 16S Rrna Gene ◽

Generation Sequencing

There is a wide array of evidence across species that exposure to antibiotics is associated with dysbiosis, and due to their widespread use, this also raises concerns also in medicine. The study aimed to determine the changes on the fecal microbiota in hospitalized neonatal foals administered with broad-spectrum antimicrobials and supplemented probiotics. Fecal samples were collected at hospital admission (Ta), at the end of the antimicrobial treatment (Te) and at discharge (Td). Feces were analysed by next-generation sequencing of the 16S rRNA gene on Illumina MiSeq. Seven foals treated with IV ampicillin and amikacin/gentamicin were included. The mean age at Ta was 19 h, the mean treatment length was 7 days and the mean time between Te and Td was 4.3 days. Seven phyla were identified: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, TM7 and Verrucomicrobia. At Ta, Firmicutes (48.19%) and Proteobacteria (31.56%) were dominant. The alpha diversity decreased from Ta to Te, but it was the highest at Td. The beta diversity was higher at Ta than at Te and higher at Td than at Te. An increase in Akkermansia over time was detected. The results suggest that the intestinal microbiota of neonatal foals rapidly returns to a high diversity after treatment. It is possible that in foals, the effect of antimicrobials is strongly influenced or overshadowed by the time-dependent changes in the developing gut microbiota.

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Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0012 ◽

2020 ◽

Vol 66 (9) ◽

pp. 495-504

Author(s):

Yan Zheng ◽

Xiaolong Hu ◽

Zhongjun Jia ◽

Paul L.E. Bodelier ◽

Zhiying Guo ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Illumina Miseq ◽

Rrna Gene ◽

Prokaryotic Community ◽

16S Rrna Gene Analysis ◽

Pit Mud ◽

Niche Competition ◽

Occurrence Patterns ◽

The 16S Rrna Gene

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.

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Impact of a Moderately Hypocaloric Mediterranean Diet on the Gut Microbiota Composition of Italian Obese Patients

Nutrients ◽

10.3390/nu12092707 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2707 ◽

Cited By ~ 1

Author(s):

Silvia Pisanu ◽

Vanessa Palmas ◽

Veronica Madau ◽

Emanuela Casula ◽

Andrea Deledda ◽

...

Keyword(s):

Gut Microbiota ◽

Mediterranean Diet ◽

Illumina Miseq ◽

Nutritional Intervention ◽

Rrna Gene ◽

Obese Patients ◽

Dietary Interventions ◽

The Impact ◽

The 16S Rrna Gene ◽

Gut Microbiota Composition

Although it is known that the gut microbiota (GM) can be modulated by diet, the efficacy of specific dietary interventions in determining its composition and diversity in obese patients remains to be ascertained. The present work aims to evaluate the impact of a moderately hypocaloric Mediterranean diet on the GM of obese and overweight patients (OB). The GM of 23 OB patients (F/M = 20/3) was compared before (T0) and after 3 months (T3) of nutritional intervention (NI). Fecal samples were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. At baseline, GM characterization confirmed typical obesity-associated dysbiosis. After 3 months of NI, patients presented a statistically significant reduction in body weight and fat mass, along with changes in the relative abundance of many microbial patterns. In fact, an increase in the abundance of several Bacteroidetes taxa (i.e., Sphingobacteriaceae, Sphingobacterium, Bacteroides spp., Prevotella stercorea) and a depletion of many Firmicutes taxa (i.e., Lachnospiraceae members, Ruminococcaceae and Ruminococcus, Veillonellaceae, Catenibacterium, Megamonas) were observed. In addition, the phylum Proteobacteria showed an increased abundance, while the genus Sutterella, within the same phylum, decreased after the intervention. Metabolic pathways, predicted by bioinformatic analyses, showed a decrease in membrane transport and cell motility after NI. The present study extends our knowledge of the GM profiles in OB, highlighting the potential benefit of moderate caloric restriction in counteracting the gut dysbiosis.

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Assessing the Effects of Ginger Extract on Polyphenol Profiles and the Subsequent Impact on the Fecal Microbiota by Simulating Digestion and Fermentation In Vitro

Nutrients ◽

10.3390/nu12103194 ◽

2020 ◽

Vol 12 (10) ◽

pp. 3194

Author(s):

Jing Wang ◽

Yong Chen ◽

Xiaosong Hu ◽

Fengqin Feng ◽

Luyun Cai ◽

...

Keyword(s):

Gut Microbiota ◽

Ph Value ◽

Illumina Miseq ◽

Short Chain Fatty Acids ◽

Fecal Microbiota ◽

Rrna Gene ◽

Gut Health ◽

Ginger Extract ◽

Mixed Culture Fermentation

The beneficial effects of ginger polyphenols have been extensively reported. However, their metabolic characteristics and health effects on gut microbiota are poor understood. The purpose of this study was to investigate the digestion stability of ginger polyphenols and their prebiotic effects on gut microbiota by simulating digestion and fermentation in vitro. Following simulated digestion in vitro, 85% of the polyphenols were still detectable, and the main polyphenol constituents identified in ginger extract are 6-, 8-, and 10-gingerols and 6-shogaol in the digestive fluids. After batch fermentation, the changes in microbial populations were measured by 16S rRNA gene Illumina MiSeq sequencing. In mixed-culture fermentation with fecal inoculate, digested ginger extract (GE) significantly modulated the fecal microbiota structure and promoted the growth of some beneficial bacterial populations, such as Bifidobacterium and Enterococcus. Furthermore, incubation with GE could elevate the levels of short-chain fatty acids (SCFAs) accompanied by a decrease in the pH value. Additionally, the quantitative PCR results showed that 6-gingerol (6G), as the main polyphenol in GE, increased the abundance of Bifidobacterium significantly. Therefore, 6G is expected to be a potential prebiotic that improves human health by promoting gut health.

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A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis

Scientific Reports ◽

10.1038/s41598-020-77054-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Davide Porcellato ◽

Roger Meisal ◽

Alberto Bombelli ◽

Judith A. Narvhus

Keyword(s):

Microbial Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Lactation Period ◽

Strong Negative Correlation ◽

Udder Health ◽

Milk Samples ◽

Lactating Cows ◽

Definition Of ◽

The 16S Rrna Gene

AbstractThe importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.

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Investigation of postpartum dairy cows’ uterine microbial diversity using metagenomic pyrosequencing of the 16S rRNA gene

Veterinary Microbiology ◽

10.1016/j.vetmic.2012.04.033 ◽

2012 ◽

Vol 159 (3-4) ◽

pp. 460-469 ◽

Cited By ~ 74

Author(s):

V.S. Machado ◽

G. Oikonomou ◽

M.L.S. Bicalho ◽

W.A. Knauer ◽

R. Gilbert ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Diversity ◽

Dairy Cows ◽

Rrna Gene ◽

The 16S Rrna Gene

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Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

10.1101/146738 ◽

2017 ◽

Cited By ~ 2

Author(s):

Garold Fuks ◽

Michael Elgart ◽

Amnon Amir ◽

Amit Zeisel ◽

Peter J. Turnbaugh ◽

...

Keyword(s):

High Resolution ◽

16S Rrna ◽

16S Rrna Gene ◽

Read Length ◽

Rrna Gene ◽

Sample Number ◽

Variable Regions ◽

Total Length ◽

Fragmented Dna ◽

The 16S Rrna Gene

AbstractBackgroundMost of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16-33% of the total length). Thus, many bacteria may share the same amplified region and the resolution of profiling is inherently limited. Platforms that offer ultra long read lengths, whole genome shotgun sequencing approaches, and computational frameworks formerly suggested by us and by others, all allow different ways to circumvent this problem yet suffer various shortcomings. There is need for a simple and low cost 16S rRNA gene based profiling approach that harnesses the short read length to provide a much larger coverage of the gene to allow for high resolution, even in harsh conditions of low bacterial biomass and fragmented DNA.ResultsThis manuscript suggests Short MUltiple Regions Framework (SMURF), a method to combine sequencing results from different PCR-amplified regions to provide one coherent profiling. The de facto amplicon length is the total length of all amplified regions, thus providing much higher resolution compared to current techniques. Computationally, the method solves a convex optimization problem that allows extremely fast reconstruction and requires only moderate memory. We demonstrate the increase in resolution by in silico simulations and by profiling two mock mixtures and real-world biological samples. Reanalyzing a mock mixture from the Human Microbiome Project achieved about two-fold improvement in resolution when combing two independent regions. Using a custom set of six primer pairs spanning about 1200bp (80%) of the 16S rRNA gene we were able to achieve ~100 fold improvement in resolution compared to a single region, over a mock mixture of common human gut bacterial isolates. Finally, profiling of a Drosophila melanogaster microbiome using the set of six primer pairs provided a ~100 fold increase in resolution, and thus enabling efficient downstream analysis.ConclusionsSMURF enables identification of near full-length 16S rRNA gene sequences in microbial communities, having resolution superior compared to current techniques. It may be applied to standard sample preparation protocols with very little modifications. SMURF also paves the way to high-resolution profiling of low-biomass and fragmented DNA, e.g., in the case of Formalin-fixed and Paraffin-embedded samples, fossil-derived DNA or DNA exposed to other degrading conditions. The approach is not restricted to combining amplicons of the 16S rRNA gene and may be applied to any set of amplicons, e.g., in Multilocus Sequence Typing (MLST).

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Resolving microbial microdiversity with high accuracy full length 16S rRNA Illumina sequencing

10.1101/010967 ◽

2014 ◽

Cited By ~ 5

Author(s):

Catherine Burke ◽

Aaron E Darling

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Single Molecule ◽

Illumina Miseq ◽

Full Length ◽

Rrna Gene ◽

Variable Regions ◽

Phylogenetic Resolution ◽

Miseq Platform ◽

The 16S Rrna Gene

We describe a method for sequencing full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform. The resulting sequences have about 100-fold higher accuracy than standard Illumina reads and are chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. We demonstrate that the data provides fine scale phylogenetic resolution not available from Illumina amplicon methods targeting smaller variable regions of the 16S rRNA gene.

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Fecal Microbiota Composition of a Mother-Infant Dyad in a Pig Model

Current Developments in Nutrition ◽

10.1093/cdn/nzaa054_087 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1015-1015

Author(s):

Julie Jeon ◽

Xi Fang ◽

Jeferson Lourenco ◽

Srujana Rayalam ◽

Michael Rothrock ◽

...

Keyword(s):

Gut Microbiome ◽

Maternal Nutrition ◽

Early Stage ◽

Illumina Miseq ◽

Well Being ◽

Fecal Microbiota ◽

Rrna Gene ◽

Gut Health ◽

Β Diversity ◽

Α Diversity

Abstract Objectives Microbial programming in early life is associated with gut health and overall well-being in adulthood. The establishment of the nascent gut microbiome is substantially influenced by both maternal nutrition and the native maternal microbiome. Pig is recognized as a valuable model in gastrointestinal track research due to its remarkable similarity to humans in gastrointestinal anatomy, physiology, biochemistry, immunology, and pathology. This study examined the characteristics of the gut microflora in the sow-piglet dyad. Methods Fecal samples were collected from sows (n = 6) and piglets (n = 24) at weaning. Bacterial DNA was isolated from the feces and the V3-V4 region of 16 s rRNA gene was amplified and sequenced using the Illumina Miseq platform and analyzed by QIIME pipeline. Results Sows had a twice higher abundance of Firmicutes than piglets (84.28% vs 40.19%, P < 0.0001), although Firmicutes was the most abundant phyla in both sows and piglets. Instead, piglets had higher abundances of Bacteroidetes (36.41% vs 9.61%, P < 0.0001) and Proteobacteria (11.31% vs 0.87%, P = 0.005) than sows. Early colonization of Proteobacteria has been suggested to be important for development of neonatal immunity. Firmicutes to Bacteroidetes ratio was higher in sows than in piglets (16.32 vs 1.36, P < 0.0001), which is consistent with previous reports in humans. The five most abundant families in sows were Clostridiaceae (30.43%), Turicibacteraceae (17.13%), Ruminococcaceae (11.29%), Lactobacillaceae (8.27%), and Lachnospiraceae (4.99%), while those in piglets were Bacteroidaceae (23.96%), Lachnospiraceae (9.13%), Clostridiaceae (7.52%), Ruminococcaceae (6.80%), and Enterobacteriaceae (6.63%). Observed OTUs in sows were higher (P = 0.02) than those in piglets, suggesting that piglets at early stage of life have lower fecal α-diversity. Moreover, β-diversity was very different between sows and piglets (P = 0.01). Conclusions Sows and piglets showed distinctive pattern of fecal microflora, and piglets had fewer species numbers at weaning compared to that of sows. This finding will provide a valuable information for future transgenerational studies on the gut microbiome and its consequences for health using a sow-piglet dyad. Funding Sources Georgia Experimental Agricultural Station, UGA Faculty research grant, and Center for Chronic Disorders of Aging at the PCOM.

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