Dynamic Changes of Intestinal Microbiota and Metabolite Composition in Pre-Weaned Beef Calves

Abstract Background: Gut microbes and their metabolites are essential for maintaining host health, but few studies have elucidated the combined effects of microbial and metabolite interactions on the growth and development of pre-weaned calves over time. Therefore, the aim of this study was to explore dynamic changes of intestinal microbiota and metabolites among newborn calves classified as healthy, sub-healthy, and those that died early during their growth and development.Results: 16S rRNA gene sequencing and metabolomics analysis was employed to track the dynamic changes in faecal microflora abundance and metabolite levels (fatty acids and amino acids) in calves before weaning. The results demonstrated that the alpha diversity of the faecal microbiota increased with calf growth and development. Specifically, the abundances of Porphyromonadaceae bacterium DJF B175 and Alistipes shahii gradually increased in healthy calves over time. Inversely, the abundance of Enterobacteriaceae was higher in the sub-healthy group than in the healthy group. Meanwhile, the faeces of calves in the early death group had significantly higher medium-long-chain fatty acid concentration than those in the healthy group. The faecal amino acid concentration decreased significantly with weekly age in the healthy and sub-healthy groups.Conclusions: The study findings provide a new understanding of calf growth and development prior to weaning. Even under the same management conditions, microorganisms and their metabolites interact to play different dynamic regulatory roles in the growth and development of newborn calves. Further studies are warranted to determine the mechanisms involved.

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Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

Frontiers in Microbiology ◽

10.3389/fmicb.2020.626713 ◽

2021 ◽

Vol 11 ◽

Author(s):

Janneke Schreuder ◽

Francisca C. Velkers ◽

Alex Bossers ◽

Ruth J. Bouwstra ◽

Willem F. de Boer ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Intestinal Microbiota ◽

Environmental Changes ◽

Temporal Dynamics ◽

Microbial Community Composition ◽

Sudden Change ◽

Rrna Gene ◽

Poultry House ◽

Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

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Biliary Microbiota and Bile Acid Composition in Cholelithiasis

BioMed Research International ◽

10.1155/2020/1242364 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Vyacheslav A. Petrov ◽

María A. Fernández-Peralbo ◽

Rico Derks ◽

Elena M. Knyazeva ◽

Nikolay V. Merzlikin ◽

...

Keyword(s):

Bile Acid ◽

Acid Composition ◽

Acid Concentration ◽

Gallstone Disease ◽

Alpha Diversity ◽

Taurocholic Acid ◽

Rrna Gene ◽

Microbial Composition ◽

Opisthorchis Felineus ◽

Taxonomic Profile

Background. A functional interplay between BAs and microbial composition in gut is a well-documented phenomenon. In bile, this phenomenon is far less studied, and with this report, we describe the interactions between the BAs and microbiota in this complex biological matrix. Methodology. Thirty-seven gallstone disease patients of which twenty-one with Opisthorchis felineus infection were enrolled in the study. The bile samples were obtained during laparoscopic cholecystectomy for gallstone disease operative treatment. Common bile acid composition was measured by LC-MS/MS. Gallbladder microbiota were previously analyzed with 16S rRNA gene sequencing on Illumina MiSeq platform. The associations between bile acid composition and microbiota were analyzed. Results. Bile acid signature and Opisthorchis felineus infection status exert influence on beta-diversity of bile microbial community. Direct correlations were found between taurocholic acid, taurochenodeoxycholic acid concentrations, and alpha-diversity of bile microbiota. Taurocholic acid and taurochenodeoxycholic acid both show positive associations with the presence of Chitinophagaceae family, Microbacterium and Lutibacterium genera, and Prevotella intermedia. Also, direct associations were identified for taurocholic acid concentration and the presence of Actinomycetales and Bacteroidales orders, Lautropia genus, Jeotgalicoccus psychrophilus, and Haemophilus parainfluenzae as well as for taurochenodeoxycholic acid and Acetobacteraceae family and Sphingomonas genus. There were no differences in bile acid concentrations between O. felineus-infected and noninfected patients. Conclusions/Significance. Associations between diversity, taxonomic profile of bile microbiota, and bile acid levels were evidenced in patients with cholelithiasis. Increase of taurochenodeoxycholic acid and taurocholic acid concentration correlates with bile microbiota alpha-diversity and appearance of opportunistic pathogens.

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The cultivation of Pyropia haitanensis has important impacts on the seawater microbial community

Journal of Applied Phycology ◽

10.1007/s10811-020-02068-6 ◽

2020 ◽

Vol 32 (4) ◽

pp. 2561-2573

Author(s):

Wenlei Wang ◽

Lei Wu ◽

Kai Xu ◽

Yan Xu ◽

Dehua Ji ◽

...

Keyword(s):

Microbial Community ◽

Growth And Development ◽

Alpha Diversity ◽

18S Rrna Gene ◽

Pyropia Haitanensis ◽

Rrna Gene ◽

Cultivation Period ◽

Rrna Gene Sequencing ◽

Bacteria And Fungi ◽

Surrounding Seawater

Abstract Microorganisms play important roles in the growth and development of macroalgae. Still, the biodiversity of the epiphytic microbial community associated with the economically important red alga Pyropia haitanensis during the cultivation period remains uncharacterized, especially the effects of P. haitanensis cultivation on the microbial community of surrounding seawater. Here, we isolated epiphytic microbes from P. haitanensis during the thallus stage during oceanic cultivation and the conchocelis stage during industrial cultivation. The dynamic diversity patterns, as determined by 16S and 18S rRNA gene sequencing of the bacterial and fungal communities, respectively, associated with P. haitanensis and seawater in the presence and absence of algal cultivation were investigated. A notable distinction was observed between the microbial communities of seawater with and without P. haitanensis cultivation. Additionally, the alpha-diversity of seawater with P. haitanensis cultivation was significantly greater than without P. haitanensis cultivation. Cyanobacteria were the dominant species in the latter, while Rhodobacteraceae was enriched in the former. Furthermore, there were significant differences in the microbial community of P. haitanensis at the thallus and conchocelis stages. Seawater properties had significant direct effects on the microbial diversity of P. haitanensis and cultivation seawater, but not on non-cultivation seawater. The enriched microbial presence might promote thallus morphogenesis and be beneficial for the growth and development of both the thallus and conchocelis stages. These findings expand our knowledge of the bacteria and fungi that are beneficial for Pyropia nursery seeding and cultivation, as well as the effects of P. haitanensis cultivation on the seawater microbial community.

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Dynamic changes in intestinal microbiota in young forest musk deer during weaning

PeerJ ◽

10.7717/peerj.8923 ◽

2020 ◽

Vol 8 ◽

pp. e8923

Author(s):

Yimeng Li ◽

Minghui Shi ◽

Tianxiang Zhang ◽

Xin Hu ◽

Baofeng Zhang ◽

...

Keyword(s):

Intestinal Microbiota ◽

Relative Abundance ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Musk Deer ◽

Dynamic Changes ◽

Linear Discriminant ◽

Bacterial Phyla ◽

Young Forest ◽

Rrna Gene Sequencing

Weaning is an important event for all mammals, including young forest musk deer. However, weaning stress may cause intestinal microbiota-related disorders. Therefore, high-throughput 16S rRNA gene sequencing was applied to study the dynamic changes in intestinal microbiota during pre-weaning (10 days before weaning) and post-weaning (10 days after weaning) in 15 young forest musk deer. We saw that intestinal microbiota diversity in the post-weaning period was significantly higher than that in the pre-weaning period. The most dominant bacterial phyla were similar in the two groups (Firmicutes, Bacteroidetes and Verrucomicrobia). Meanwhile, we applied Linear discriminant analysis effect size (LefSe) to identify the most differentially microbial taxa in the pre-weaning and post-weaning groups. In the post-weaning forest musk deer, the relative abundance of Actinobacteria, Spirochaetes, Ruminococcaceae_UCG-005, Treponema and Prevotella was higher than in the pre-weaning group. However, higher relative abundance of the phyla Bacteroidetes was found in the pre-weaning group compared with that in the post-weaning group. In summary, this research provides a theoretical foundation for the dynamics of young forest musk deer intestinal microbiota during the weaning transition, which may benefit in understanding the growth and health of forest musk deer.

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Biliary microbiota and bile acids composition in cholelithiasis

10.1101/469825 ◽

2018 ◽

Author(s):

Vyacheslav A. Petrov ◽

María A. Fernández-Peralbo ◽

Rico Derks ◽

Elena M. Knyazeva ◽

Nikolay V. Merzlikin ◽

...

Keyword(s):

Microbial Community ◽

Bile Acids ◽

Acid Concentration ◽

Gallstone Disease ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Taurocholic Acid ◽

Rrna Gene ◽

Microbial Composition ◽

Taxonomic Profile

AbstractBackgroundA functional interplay between BAs and microbial composition in gut is a well-documented phenomenon. In bile this phenomenon is far less studied and with this report we describe the interactions between the BAs and microbiota in this complex biological matrix.MethodologyThirty-seven gallstone disease patients of which twenty-one withOpisthorchis felineusinfection were enrolled in the study. The bile samples were obtained during laparoscopic cholecystectomy for gallstone disease operative treatment. Common bile acids composition were measured by LC-MS/MS using a column in reverse phase. For all patients gallbladder microbiota was previously analyzed with 16S rRNA gene sequencing on Illumina MiSeq platform. The associations between bile acids composition and microbiota were analysed.Principal findingsBile acids signature andO. felineusinfection status exerts influence on beta-diversity of bile microbial community. Direct correlations were found between taurocholic acid, taurochenodeoxycholic acid concentrations and alpha-diversity of bile microbiota. Taurocholic acid and taurochenodeoxycholic acid both shows positive associations with the presence of Chitinophagaceae family,MicrobacteriumandLutibacteriumgenera andPrevotella intermedia. Also direct associations were identified for taurocholic acid concentration and the presence of Actinomycetales and Bacteroidales orders,Lautropiagenus,Jeotgalicoccus psychrophilusandHaemophilus parainfluenzaeas well as for taurochenodeoxycholic acid and Acetobacteraceae family and Sphingomonas genus. There were no differences in bile acids concentrations between O.felineusinfected and non-infected patients.Conclusions/SignificanceAssociations between diversity, taxonomic profile of bile microbiota and bile acids levels were evidenced in patients with cholelithiasis. Increase of taurochenodeoxycholic acid and taurocholic acid concentration correlates with bile microbiota alpha-diversity and appearance of opportunistic pathogens. Alteration of bile acids signature could cause shifts in bile microbial community structure.

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Effects of Smoking and Smoking Cessation on the Intestinal Microbiota

Journal of Clinical Medicine ◽

10.3390/jcm9092963 ◽

2020 ◽

Vol 9 (9) ◽

pp. 2963

Author(s):

Marcus G. Sublette ◽

Tzu-Wen L. Cross ◽

Claudia E. Korcarz ◽

Kristin M. Hansen ◽

Sofia M. Murga-Garrido ◽

...

Keyword(s):

Smoking Cessation ◽

Intestinal Microbiota ◽

Disease Risk ◽

Cardiovascular Disease Risk ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Alpha And Beta Diversity ◽

Quit Attempt ◽

Relative Abundances

We evaluated associations of smoking heaviness markers and the effects of smoking cessation on the intestinal microbiota and cardiovascular disease risk factors in current smokers undertaking a quit attempt. Participants were current smokers enrolled in a prospective randomized clinical trial of smoking cessation therapies with visits at baseline, 2, and 12 weeks. Genomic DNA was extracted from fecal samples followed by 16S rRNA gene sequencing and analysis using the QIIME2 software workflow. Relative abundances of bacterial taxa and alpha- and beta-diversity measures were used for comparisons. The 36 smokers were (mean (standard deviation)) 51.5 (11.1) years old (42% male) and smoked 15.1 (6.4) cigarettes per day for 22.7 (11.9) pack-years. Relative abundances of the phylum Actinobacteria correlated with pack-years (rho = −0.44, p = 0.008) and Cyanobacteria correlated with CO levels (rho = 0.39, p = 0.021). After 12 weeks, relative abundances of the phylum Bacteroidetes increased (pANCOVA = 0.048) and Firmicutes decreased (pANCOVA = 0.036) among abstainers compared to continuing smokers. Increases in alpha-diversity were associated with heart rates (rho = −0.59, p = 0.037), systolic blood pressures (rho = −0.58, p = 0.043), and C-reactive protein (rho = −0.60, p = 0.034). Smoking cessation led to minor changes in the intestinal microbiota. It is unclear if the proven health benefits of smoking cessation lead to salutary changes in the intestinal microbiota.

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Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

Animal Microbiome ◽

10.1186/s42523-019-0017-z ◽

2019 ◽

Vol 1 (1) ◽

Cited By ~ 3

Author(s):

Laura Glendinning ◽

Kellie A. Watson ◽

Mick Watson

Keyword(s):

Microbial Community ◽

Intestinal Microbiota ◽

Intestinal Tract ◽

Microbial Community Composition ◽

Intestinal Content ◽

Rrna Gene ◽

Large Role ◽

The 16S Rrna Gene ◽

Caecal Microbiota ◽

Over Time

Abstract Background The chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare. Results In this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identified significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterised the development of the microbiota at each intestinal site over time. Conclusions Our study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

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Species-Level Gut Microbiota Analysis after Antibiotic-Induced Dysbiosis in Horses

Animals ◽

10.3390/ani11102859 ◽

2021 ◽

Vol 11 (10) ◽

pp. 2859

Author(s):

Rebecca Di Pietro ◽

Luis G. Arroyo ◽

Mathilde Leclere ◽

Marcio Carvalho Costa

Keyword(s):

Gut Microbiota ◽

Intestinal Microbiota ◽

Illumina Sequencing ◽

Alpha Diversity ◽

Species Level ◽

Rrna Gene ◽

Antibiotic Administration ◽

Before And After ◽

Long Read ◽

Equine Studies

All current studies have used Illumina short-read sequencing to characterize the equine intestinal microbiota. Long-read sequencing can classify bacteria at the species level. The objectives of this study were to characterize the gut microbiota of horses at the species level before and after trimethoprim sulfadiazine (TMS) administration and to compare results with Illumina sequencing. Nine horses received TMS (30 mg/kg) orally for 5 days twice a day to induce dysbiosis. Illumina sequencing of the V4 region or full-length PacBio sequencing of the 16S rRNA gene was performed in fecal samples collected before and after antibiotic administration. The relative abundance and alpha diversity were compared between the two technologies. PacBio failed to classify the equine intestinal microbiota at the species level but confirmed Bacteroidetes as the most abundant bacteria in the feces of the studied horses, followed by Firmicutes and Fibrobacteres. An unknown species of the Bacteroidales order was highly abundant (13%) and deserves further investigation. In conclusion, PacBio was not suitable to classify the equine microbiota species but detected greater richness and less unclassified bacteria. Further efforts in improving current databanks to be used in equine studies are necessary.

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Assessing saliva microbiome collection and processing methods

npj Biofilms and Microbiomes ◽

10.1038/s41522-021-00254-z ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Abigail J. S. Armstrong ◽

Veenat Parmar ◽

Martin J. Blaser

Keyword(s):

Alpha Diversity ◽

Shotgun Sequencing ◽

Oral Microbiome ◽

Rrna Gene ◽

Shotgun Metagenomics ◽

Human Dna ◽

Within Subjects ◽

Saliva Collection ◽

Lung Health ◽

Over Time

AbstractThe oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.

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Impairments of the intestinal microbiota in the acute period of infectious diarrhea in children and comparative analysis of the effects of nifuroxazide and cephalosporins

Infekcionnye bolezni ◽

10.20953/1729-9225-2020-3-88-96 ◽

2020 ◽

Vol 18 (3) ◽

pp. 88-96

Author(s):

D.V. Usenko ◽

◽

A.V. Gorelov ◽

V.E. Odintsova ◽

D.A. Kashtanova ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Intestinal Microbiota ◽

Alpha Diversity ◽

Control Group ◽

Rrna Gene ◽

Healthy Children ◽

Infectious Diarrhea ◽

Opportunistic Bacteria ◽

Intestinal Infections

The intestinal microbiota (IM) plays an important role in maintaining homeostasis in the human organism. Changes in the IM are associated with many diseases, for example, IM is involved in the pathogenesis of inflammation during acute intestinal infections (AIIs). Medications have different effects on the quantitative and qualitative composition of the microbial community and can therefore indirectly affect the course of recovery. Objective. To evaluate the IM composition in the acute period of infectious diarrhea in children and to assess the effect of therapy with nifuroxazide and cephalosporins on it. Patients and methods. This study included 21 children with invasive AIIs. Twelve patients received nifuroxazide (IN group), whereas 9 patients were treated with third-generation cephalosporins (IC group). There was also a control group comprised of 10 healthy children (group C). The duration of the course of antibacterial therapy was 5–7 days. We analyzed the microbial composition of fecal specimens from all study participants using 16S rRNA gene high-throughput sequencing. Data analysis was performed using the Knomics-Biota platform and the R Programming Environment. Results. We observed reduced alpha diversity (an integral characteristic of a microbial community which estimates the number of species in it and their proportion) already in the early period of invasive AII in children. We also found an increased total proportion of opportunistic bacteria in children with AIIs compared to controls, particularly species of Fusobacteriacea. Restoration of alpha diversity was achieved only in patients receiving nifuroxazide. Differences in the dynamics of the proportion of opportunistic microflora in the intervention groups were associated with the initial differences in the microbiome composition between the groups due to small number of patients in them. In the IN group, the proportion of Fusobacteriaceae species before treatment was higher than that in healthy controls; however, immediately after treatment completion and one month later, there were no differences in the IM composition between the IN group and controls. Patients from the IC group had higher proportion of opportunistic bacteria than healthy children; by the end of the treatment course, this parameter was normalized and was similar to that in the control group. Conclusion. The use of nifuroxazide in children with invasive AIIs was associated with restoration of alpha diversity and the reduction in the proportion of opportunistic species (in particular, Fusobacteriaceae). Children receiving cephalosporins also demonstrated the reduction in this proportion, but their alpha diversity was not restored. Keywords: acute intestinal infections, children, antibacterial therapy, nifuroxazide, cephalosporins, intestinal microbiota, 16S rRNA gene sequencing

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