Microbiome Analysis Reveals the Dynamic Alternations in Gut Microbiota of Diarrheal Giraffa camelopardalis

The ruminant gut microbial community's importance has been widely acknowledged due to its positive roles in physiology, metabolism, and health maintenance. Diarrhea has been demonstrated to cause adverse effects on gastrointestinal health and intestinal microecosystem, but studies regarding diarrheal influence on gut microbiota in Giraffa camelopardalis have been insufficient to date. Here, this study was performed to investigate and compare gut microbial composition and variability between healthy and diarrheic G. camelopardalis. The results showed that the gut microbial community of diarrheal G. camelopardalis displayed a significant decrease in alpha diversity, accompanied by distinct alterations in taxonomic compositions. Bacterial taxonomic analysis indicated that the dominant bacterial phyla (Proteobacteria, Bacteroidetes, and Firmicutes) and genera (Escherichia Shigella and Acinetobacter) of both groups were the same but different in relative abundance. Specifically, the proportion of Proteobacteria in the diarrheal G. camelopardalis was increased as compared with healthy populations, whereas Bacteroidetes, Firmicutes, Tenericutes, and Spirochaetes were significantly decreased. Moreover, the relative abundance of one bacterial genus (Comamonas) dramatically increased in diarrheic G. camelopardalis, whereas the relative richness of 18 bacterial genera decreased compared with healthy populations. Among them, two bacterial genera (Ruminiclostridium_5 and Blautia) cannot be detected in the gut bacterial community of diarrheal G. camelopardalis. In summary, this study demonstrated that diarrhea could significantly change the gut microbial composition and diversity in G. camelopardalis by increasing the proportion of pathogenic to beneficial bacteria. Moreover, this study first characterized the distribution of gut microbial communities in G. camelopardalis with different health states. It contributed to providing a theoretical basis for establishing a prevention and treatment system for G. camelopardalis diarrhea.

Download Full-text

PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

Journal of Animal Science ◽

10.1093/jas/skz258.594 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 293-294

Author(s):

Camila S Marcolla ◽

Benjamin Willing

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Poultry Production ◽

Microbiota Composition ◽

Microbial Composition ◽

The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

Download Full-text

Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola

Frontiers in Microbiology ◽

10.3389/fmicb.2021.699699 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yu Huang ◽

Han-Cheng Wang ◽

Liu-Ti Cai ◽

Wenhong Li ◽

Daiwei Pan ◽

...

Keyword(s):

Disease Severity ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Abiotic Factors ◽

Alpha Diversity ◽

Disease Index ◽

Microbial Composition ◽

Tobacco Leaves ◽

Tobacco Leaf ◽

Bacterial Phyla

A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.

Download Full-text

Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

Journal of Personalized Medicine ◽

10.3390/jpm11040294 ◽

2021 ◽

Vol 11 (4) ◽

pp. 294

Author(s):

Irina Grigor’eva ◽

Tatiana Romanova ◽

Natalia Naumova ◽

Tatiana Alikina ◽

Alexey Kuznetsov ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Gallstone Disease ◽

Illumina Miseq ◽

Rrna Gene ◽

Bacterial Phyla ◽

Female Patients ◽

Composition And Structure ◽

Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

Download Full-text

Impact of the gut microbiome on the atorvastatin-dependent modulation of the serum lipidome

European Heart Journal ◽

10.1093/ehjci/ehaa946.3823 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

J Roessler ◽

F Zimmermann ◽

D Schmidt ◽

U Escher ◽

A Jasina ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Interindividual Variation ◽

Funding Source ◽

Microbial Composition ◽

Atorvastatin Treatment ◽

Qrt Pcr ◽

16S Rna ◽

Regulatory Properties

Abstract Background and aims The modulation of serum lipids, in particular of the low-density lipoprotein cholesterol (LDL-C), by statins varies between individuals. The mechanisms regulating this interindividual variation are only poorly understood. Here, we investigated the relation between the gut microbiome and the regulatory properties of atorvastatin on the serum lipidome using mice with depleted gut microbiome. Methods Over a period of 6 weeks, mice (C57BL/6) with either an intact (conventional mice, CONV, n=24) or antibiotic-based depleted gut microbiome (antibiotic treated mice, ABS, n=16) were put on standard chow diet (SCD) or high fat diet (HFD), respectively. During the last 4 weeks of treatment atorvastatin (Ator, 10mg/kg body weight/day) or control vehicle was administered via daily oral gavage. Blood lipids (total cholesterol, VLDL, LDL-C, HDL-C) and serum sphingolipids were compared among the groups. The expressions of hepatic and intestinal genes involved in cholesterol metabolism were analyzed by qRT-PCR. Alterations in the gut microbiota profile of mice with intact gut microbiome were examined using 16S RNA qRT-PCR. Results In CONV mice, HFD led to significantly increased blood LDL-C levels as compared with SCD (HFD: 36.8±1.4 mg/dl vs. SCD: 22.0±1.8 mg/dl; P<0.01). In CONV mice atorvastatin treatment significantly reduced blood LDL-C levels after HFD, whereas in ABS mice the LDL-C lowering effect of atorvastatin was markedly attenuated (CONV+HFD+Ator: 31.0±1.8 mg/dl vs. ABS+HFD+Ator: 46.4±3 mg/dl; P<0.01). A significant reduction in the abundance of several plasma lipids, in particular sphingolipids and glycerophospholipids upon atorvastatin treatment was observed in CONV mice, but not in ABS mice. The expressions of distinct hepatic and intestinal cholesterol-regulating genes (ldlr, srebp2, pcsk9 and npc1l1) upon atorvastatin treatment were significantly altered in gut microbiota depleted mice. In response to HFD a decrease in the relative abundance of the bacterial phyla Bacteroides and an increase in the relative abundance of Firmicutes was observed. The altered ratio between Bacteroides and Firmicutes in HFD fed mice was partly reversed upon atorvastatin treatment. Conclusions Our findings indicate a crucial role of the gut microbiome for the regulatory properties of atorvastatin on the serum lipidome and, in turn, support a critical impact of atorvastatin on the gut microbial composition. The results provide novel insights into potential microbiota related mechanisms underlying interindividual variation in modulation of the serum lipidome by statins, given interindividual differences in microbiome composition and function. Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): German Heart Research Foundation

Download Full-text

The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota

Microorganisms ◽

10.3390/microorganisms9020278 ◽

2021 ◽

Vol 9 (2) ◽

pp. 278

Author(s):

Shen Jean Lim ◽

Miriam Aguilar-Lopez ◽

Christine Wetzel ◽

Samia V. O. Dutra ◽

Vanessa Bray ◽

...

Keyword(s):

Gut Microbiota ◽

Preterm Infant ◽

Neonatal Intensive Care ◽

Genetic Relatedness ◽

Bovine Milk ◽

Alpha Diversity ◽

Neonatal Intensive Care Units ◽

Rrna Gene ◽

Microbial Composition ◽

Operational Taxonomic Units

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

Download Full-text

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Biology ◽

10.3390/biology10030180 ◽

2021 ◽

Vol 10 (3) ◽

pp. 180

Author(s):

Negash Kabtimer Bereded ◽

Getachew Beneberu Abebe ◽

Solomon Workneh Fanta ◽

Manuel Curto ◽

Herwig Waidbacher ◽

...

Keyword(s):

Gut Microbiota ◽

Nile Tilapia ◽

Alpha Diversity ◽

Environmental Parameters ◽

Illumina Miseq ◽

Microbial Composition ◽

Lake Tana ◽

Future Work ◽

The Impact ◽

Sampling Season

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Download Full-text

Gut Microbiota Shifts Favorably with Delivery of Handwashing with Soap and Water Treatment Intervention in a Prospective Cohort (CHoBI7 Trial)

10.21203/rs.3.rs-752679/v1 ◽

2021 ◽

Author(s):

Shirajum Monira ◽

Indrajeet Barman ◽

Fatema Tuz Jubyda ◽

Sk. Imran Ali ◽

Aminul Islam ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Controlled Trial ◽

Elevated Risk ◽

Great Promise ◽

Treatment Intervention ◽

Bacterial Phyla ◽

Household Contacts ◽

Randomized Controlled ◽

Handwashing With Soap

Abstract Cholera can result in the expulsion of important microbiota from the gut and result in death if left untreated. The disease transmits mainly via drinking water carrying Vibrio cholerae; and household contacts (HHC) of cholera patients are at elevated risk during the first week of infection. The gut microbiota profiles of HHC-children of cholera patients at Dhaka city slums were investigated before (day 0) and after (day 8) delivery of chlorinated water as part of the cholera-hospital-based intervention for 7 days (CHoBI7), a randomized controlled trial. Results of sequencing and analysis of bacterial community DNA revealed the predominance of two bacterial phyla: Bacteroidetes and Firmicutes at day 0 with a relative abundance of 62 ± 6 (mean ± SEM %) and 32 ± 7, respectively. The pattern reversed at day 8 with a decreased relative abundance of Bacteroidetes (39 ± 12) and an increased abundance of Firmicutes (49 ± 12). Of 65 bacterial families confirmed at day 0, six belonging to Proteobacteria including Vibrionaceae disappeared at day 8. Interestingly, the relative abundance of four Firmicutes families– Lachnospiraceae, Bifidobacteriaceae, Clostridiaceae, and Ruminococcaceae was increased in all five study children at day 8. The observed exclusion of pathogenic Proteobacteria and enhancement of beneficial Firmicutes in the gut of children delivered with chlorinated water as part of WASH intervention reflect a great promise of the CHoBI7 program in preventing cholera and improving child health.

Download Full-text

Probiotic Supplementation in a Clostridium difficile-Infected Gastrointestinal Model Is Associated with Restoring Metabolic Function of Microbiota

Microorganisms ◽

10.3390/microorganisms8010060 ◽

2019 ◽

Vol 8 (1) ◽

pp. 60

Author(s):

Mohd Baasir Gaisawat ◽

Chad W. MacPherson ◽

Julien Tremblay ◽

Amanda Piano ◽

Michèle M. Iskandar ◽

...

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

Gastrointestinal Disorder ◽

Short Chain Fatty Acids ◽

Rrna Gene ◽

Metabolic Function ◽

Microbial Composition ◽

Single Strain ◽

Fecal Samples ◽

Metabolic Functions

Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an adjunct is being studied extensively due to their potential to modulate metabolic functions and the gut microbiota. In the present study, we assessed the ability of several single strain probiotics and a probiotic mixture to change the metabolic functions of normal and C. difficile-infected fecal samples. The production of short-chain fatty acids (SCFAs), hydrogen sulfide (H2S), and ammonia was measured, and changes in microbial composition were assessed by 16S rRNA gene amplicon sequencing. The C. difficile-infection in fecal samples resulted in a significant decrease (p < 0.05) in SCFA and H2S production, with a lower microbial alpha diversity. All probiotic treatments were associated with significantly increased (p < 0.05) levels of SCFAs and restored H2S levels. Probiotics showed no effect on microbial composition of either normal or C. difficile-infected fecal samples. These findings indicate that probiotics may be useful to improve the metabolic dysregulation associated with C. difficile infection.

Download Full-text

Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats

Physiological Genomics ◽

10.1152/physiolgenomics.00039.2020 ◽

2020 ◽

Vol 52 (7) ◽

pp. 280-292 ◽

Cited By ~ 4

Author(s):

Katherine A. Maki ◽

Larisa A. Burke ◽

Michael W. Calik ◽

Miki Watanabe-Chailland ◽

Dagmar Sweeney ◽

...

Keyword(s):

Blood Pressure ◽

Mean Arterial Pressure ◽

Gut Microbiota ◽

Arterial Pressure ◽

Gut Microbiome ◽

Alpha Diversity ◽

Sleep Fragmentation ◽

Cardiovascular Pathology ◽

Acid Producing Bacteria ◽

Gut Microbial Community

The gut microbiota, via the production of metabolites entering the circulation, plays a role in blood pressure regulation. Blood pressure is also affected by the characteristics of sleep. To date, no studies have examined relationships among the gut microbiota/metabolites, blood pressure, and sleep. We hypothesized that fragmented sleep is associated with elevated mean arterial pressure, an altered and dysbiotic gut microbial community, and changes in fecal metabolites. In our model system, rats were randomized to 8 h of sleep fragmentation during the rest phase (light phase) or were undisturbed (controls) for 28 consecutive days. Rats underwent sleep and blood pressure recordings, and fecal samples were analyzed during: baseline ( days −4 to −1), early sleep fragmentation ( days 0–3), midsleep fragmentation ( days 6–13), late sleep fragmentation ( days 20–27), and recovery/rest ( days 28–34). Less sleep per hour during the sleep fragmentation period was associated with increased mean arterial pressure. Analyses of gut microbial communities and metabolites revealed that putative short chain fatty acid-producing bacteria were differentially abundant between control and intervention animals during mid-/late sleep fragmentation and recovery. Midsleep fragmentation was also characterized by lower alpha diversity, lower Firmicutes:Bacteroidetes ratio, and higher Proteobacteria in intervention rats. Elevated putative succinate-producing bacteria and acetate-producing bacteria were associated with lower and higher mean arterial pressure, respectively, and untargeted metabolomics analysis demonstrates that certain fecal metabolites are significantly correlated with blood pressure. These data reveal associations between sleep fragmentation, mean arterial pressure, and the gut microbiome/fecal metabolome and provide insight to links between disrupted sleep and cardiovascular pathology.

Download Full-text

Bacillus licheniformis Zhengchangsheng® attenuates DSS-induced colitis and modulates the gut microbiota in mice

Beneficial Microbes ◽

10.3920/bm2018.0122 ◽

2019 ◽

Vol 10 (5) ◽

pp. 543-553 ◽

Cited By ~ 3

Author(s):

Y. Li ◽

M. Liu ◽

J. Zhou ◽

B. Hou ◽

X. Su ◽

...

Keyword(s):

Gut Microbiota ◽

Bacillus Licheniformis ◽

Activity Index ◽

Intestinal Barrier ◽

Disease Activity Index ◽

Experimental Colitis ◽

Valuable Insight ◽

Microbial Composition ◽

Gastrointestinal Health ◽

Human Inflammatory Bowel Disease

Human inflammatory bowel disease (IBD) and experimental colitis models in mice are associated with shifts in gut microbiota composition, and several probiotics are widely used to improve gastrointestinal health. Here, we investigated whether the probiotic Bacillus licheniformis Zhengchangsheng® (BL) ameliorates dextran sulphate sodium (DSS)-induced colitis through alteration of the gut microbiota. Experimental colitis was induced in BALB/C mice by dissolving 3% DSS in their drinking water for 7 days, which were gavaged with 0.2 ml phosphate-buffered saline or BL (3×107 cfu/ml) once a day. Administration of BL attenuated several effects of DSS-induced colitis, including weight loss, increased disease activity index, and disrupted intestinal barrier integrity. In addition, BL mitigated the reduction in faecal microbiota richness in DSS treated mice. Interestingly, BL was found to reduce the elevated circulating endotoxin level in mice with colitis by modulating the microbial composition of the microbiota, and this was highly associated with a proportional decrease in gut Bacteroidetes. Our results demonstrate that BL can attenuate DSS-induced colitis and provide valuable insight into microbiota interactions during IBD.

Download Full-text