scholarly journals Environmental Impact on Differential Composition of Gut Microbiota in Indoor Chickens in Commercial Production and Outdoor, Backyard Chickens

2020 ◽  
Vol 8 (5) ◽  
pp. 767
Author(s):  
Zuzana Seidlerova ◽  
Tereza Kubasova ◽  
Marcela Faldynova ◽  
Magdalena Crhanova ◽  
Daniela Karasova ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Extreme Environments ◽  
Antibiotic Resistance Genes ◽  
Commercial Production ◽  
Living Environment ◽  
Egg Laying ◽  
Microbiota Composition ◽  
Feed Composition ◽  
Caecal Microbiota ◽  
Indoor And Outdoor

In this study, we compared the caecal microbiota composition of egg-laying hens from commercial production that are kept indoors throughout their whole life with microbiota of hens kept outdoors. The microbiota of outdoor hens consisted of lower numbers of bacterial species than the microbiota of indoor hens. At the phylum level, microbiota of outdoor hens was enriched for Bacteroidetes (62.41 ± 4.47% of total microbiota in outdoor hens and 52.01 ± 6.27% in indoor hens) and Proteobacteria (9.33 ± 4.99% in outdoor and 5.47 ± 2.24% in indoor hens). On the other hand, Firmicutes were more abundant in the microbiota of indoor hens (33.28 ± 5.11% in indoor and 20.66 ± 4.41% in outdoor hens). Horizontally transferrable antibiotic resistance genes tetO, tet(32), tet(44), and tetW were also less abundant in the microbiota of outdoor hens than indoor hens. A comparison of the microbiota composition at the genus and species levels pointed toward isolates specifically adapted to the two extreme environments. However, genera and species recorded as being similarly abundant in the microbiota of indoor and outdoor hens are equally as noteworthy because these represent microbiota members that are highly adapted to chickens, irrespective of their genetics, feed composition, and living environment.

The Effects of Increasing Intake of Intact Wheat Fibre or Wheat Bran on Gut Microbiota Diversity: a Systematic Review

2020 ◽  
Vol 79 (OCE2) ◽  
Author(s):  
Angie Jefferson ◽  
Katie Adolphus
Keyword(s):  
Systematic Review ◽  
Gut Microbiota ◽  
Wheat Bran ◽  
Bacterial Species ◽  
Microbiota Composition ◽  
Inclusion Criteria ◽  
Breakfast Cereal ◽  
High Fibre ◽  
Microbiota Diversity ◽  
Gut Microbiota Composition

AbstractThe influence on health of the human gut microbiota is increasingly recognised, however wheat fibre, consumed frequently in Western diets has traditionally been considered inert with regard to gut microbiota composition and metabolic activity. We undertook a systematic review (PRISMA methodology) of human intervention studies examining the effects of intact cereal fibres on gut microbiota composition among healthy adults.(1) Studies published in the past 20 years were identified on PubMed and Cochrane electronic databases. Inclusion criteria were: healthy adult participants, at least one intact cereal fibre (or its sub-fraction) and measurement of faecal microbiota related outcomes. Out of forty studies meeting inclusion criteria, seventeen manipulated wheat fibre/bran or its key constituent arabinoxylans (AXOS), and ten used a whole diet approach with predominantly wheat fibre. Results from these twenty seven wheat fibre papers are presented here. Eight studies provided wheat bran/fibre (ranging from 5.7g-21g/day wheat fibre or 13g-28g/day wheat bran). Three reported significant effects on gut microbiota abundance and/or diversity (both at phyla and species level) and one showed no effect. Six reported significant increases in fermentation metabolites and one reported no significant change. Ten studies manipulated whole day fibre intake (predominantly wheat but also permitting some oats, rye and rice). Wholegrain intake ranged from 80g-150 g per day and fibre from 13.7g–40 g per day. Six found significant increases in bacterial diversity and/or abundance and five showed significant increases in fermentation metabolites. Two identified that response to high fibre intervention is dependent on baseline gut microbiota richness - those with limited richness exhibiting greater microbiota change over time in response to fibre increase. Two reported no significant effects. Nine studies utilised manipulation of AXOS (2.2g–18.8 g per day) with five demonstrating significant increases in target bacterial species and six significant increases in fermentation metabolites. One reported no significant effect to faecal metabolites. This review supports a role for the wheat fibre found in everyday foods (such as bran breakfast cereal of high fibre breads) promoting both microbiota diversity and abundance. While the healthy microbiome is yet to be defined, consumption of a single daily serving of wheat bran fibre appears sufficient to effect gut microbiota fermentation (with demonstrable effects arising from as low as 6g/day), and promote species diversity, with potential benefit to health.However exploration of stability over longer time frames (> 12 weeks) is now required.

scholarly journals Postnatal development of the rabbit caecal microbiota composition and activity

2011 ◽  
Vol 77 (3) ◽  
pp. 680-689 ◽  
Author(s):  
Sylvie Combes ◽  
Rory Julien Michelland ◽  
Valérie Monteils ◽  
Laurent Cauquil ◽  
Vincent Soulié ◽  
...  
Keyword(s):  
Postnatal Development ◽  
Microbiota Composition ◽  
Caecal Microbiota

scholarly journals Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment

2021 ◽  
Author(s):  
Peng Zhang ◽  
Daqing Mao ◽  
Huihui Gao ◽  
Liyang Zheng ◽  
Zeyou Chen ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Evolutionary Adaptation ◽  
Antibiotic Exposure ◽  
Resistance Protein ◽  
K 12

AbstractMultidrug-resistant plasmid-carrying bacteria are of particular clinical concern as they could transfer antibiotic resistance genes to other bacterial species. However, little is known whether evolutionary adaptation of plasmid-carrying bacteria after long-term antibiotic exposure could affect their subsequent colonization of the human gut. Herein, we combined a long-term evolutionary model based on Escherichia coli K-12 MG1655 and the multidrug-resistant plasmid RP4 with in vivo colonization experiments in mice. We found that the evolutionary adaptation of plasmid-carrying bacteria to antibiotic exposure facilitated colonization of the murine gut and subsequent plasmid transfer to gut bacteria. The evolved plasmid-carrying bacteria exhibited phenotypic alterations, including multidrug resistance, enhanced bacterial growth and biofilm formation capability and decreased plasmid fitness cost, which might be jointly caused by chromosomal mutations (SNPs in rpoC, proQ, and hcaT) and transcriptional modifications. The upregulated transcriptional genes, e.g., type 1 fimbrial-protein pilus (fimA and fimH) and the surface adhesin gene (flu) were likely responsible for the enhanced biofilm-forming capacity. The gene tnaA that encodes a tryptophanase-catalyzing indole formation was transcriptionally upregulated, and increased indole products participated in facilitating the maximum population density of the evolved strains. Furthermore, several chromosomal genes encoding efflux pumps (acriflavine resistance proteins A and B (acrA, acrB), outer-membrane protein (tolC), multidrug-resistance protein (mdtM), and macrolide export proteins A and B (macA, macB)) were transcriptionally upregulated, while most plasmid-harboring genes (conjugal transfer protein (traF) and (trbB), replication protein gene (trfA), beta-lactamase TEM precursor (blaTEM), aminoglycoside 3'-phosphotransferase (aphA) and tetracycline resistance protein A (tetA)) were downregulated. Collectively, these findings demonstrated that evolutionary adaptation of plasmid-carrying bacteria in an antibiotic-influenced environment facilitated colonization of the murine gut by the bacteria and plasmids.

scholarly journals Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Sarah Entwistle ◽  
Xueqiong Li ◽  
Yanbin Yin
Keyword(s):  
Bacterial Species ◽  
Single Species ◽  
Living Environment ◽  
Open Reading Frames ◽  
Orphan Genes ◽  
Bacterial Pathogenicity ◽  
Therapeutic Drugs ◽  
New Genes ◽  
Its Gene ◽  
The Comparative Study

ABSTRACT Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)—including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)—than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity. IMPORTANCE Recent pangenome analyses of numerous bacterial species have suggested that each genome of a single species may have a significant fraction of its gene content unique or shared by a very few genomes (i.e., ORFans). We selected nine bacterial genera, each containing at least five pathogenic and five nonpathogenic genomes, to compare their ORFans in relation to pathogenicity-related genes. Pathogens in these genera are known to cause a number of common and devastating human diseases such as pneumonia, diphtheria, melioidosis, and tuberculosis. Thus, they are worthy of in-depth systems microbiology investigations, including the comparative study of ORFans between pathogens and nonpathogens. We provide direct evidence to suggest that ORFans shared by more pathogens are more associated with pathogenicity-related genes and thus are more important targets for development of new diagnostic markers or therapeutic drugs for bacterial infectious diseases.

scholarly journals Effects of monobutyrin and tributyrin on liver lipid profile, caecal microbiota composition and SCFA in high-fat diet-fed rats

2017 ◽  
Vol 6 ◽  
Author(s):  
Thao Duy Nguyen ◽  
Olena Prykhodko ◽  
Frida Fåk Hållenius ◽  
Margareta Nyman
Keyword(s):  
Succinic Acid ◽  
High Fat Diet ◽  
Intestinal Tract ◽  
Liver Lipid ◽  
Microbiota Composition ◽  
Risk Markers ◽  
High Fat ◽  
High Fat Diets ◽  
Fat Diets ◽  
Caecal Microbiota

AbstractButyric acid has been shown to have suppressive effects on inflammation and diseases related to the intestinal tract. The aim of the present study was to investigate whether supplementation of two glycerol esters, monobutyrin (MB) and tributyrin (TB), would reach the hindgut of rats, thus having an effect on the caecal profile of SCFA, microbiota composition and some risk markers associated with chronic inflammation. For this purpose, rats were fed high-fat diets after adding MB (1 and 5 g/kg) and TB (5 g/kg) to a diet without any supplementation (high-fat control; HFC). A low-fat (LF) diet was also included. In the liver, total cholesterol concentrations, LDL-cholesterol concentrations, LDL:HDL ratio, and succinic acid concentrations were reduced in rats given the MB and TB (5 g/kg) diets, compared with the group fed the HFC diet. These effects were more pronounced in MB than TB groups as also expressed by down-regulation of the gene Cyp8b1. The composition of the caecal microbiota in rats fed MB and TB was separated from the group fed the HFC diet, and also the LF diet, as evidenced by the absence of the phylum TM7 and reduced abundance of the genera Dorea (similar to LF-fed rats) and rc4-4. Notably, the caecal abundance of Mucispirillum was markedly increased in the MB group compared with the HFC group. The results suggest that dietary supplementation of MB and TB can be used to counteract disturbances associated with a HFC diet, by altering the gut microbiota, and decreasing liver lipids and succinic acid concentrations.

Evaluation of the efficacy of sequential or continuous administration of probiotics and phytogenics in broiler diets

2015 ◽  
Vol 55 (6) ◽  
pp. 720 ◽  
Author(s):  
K. C. Mountzouris ◽  
P. Tsirtsikos ◽  
G. Papadomichelakis ◽  
G. Schatzmayr ◽  
K. Fegeros
Keyword(s):  
Basal Diet ◽  
Time Frame ◽  
Bodyweight Gain ◽  
Nutrient Digestibility ◽  
Molar Ratio ◽  
Microbiota Composition ◽  
Feed Conversion ◽  
Continuous Administration ◽  
Experimental Treatments ◽  
Caecal Microbiota

Three dietary combinations of probiotics and phytogenics administered sequentially or continuously were assessed for their effects on broiler performance, nutrient digestibility, caecal microbiota composition, volatile fatty acid (VFA) pattern and plasma total antioxidant capacity (TAC). One-day-old Cobb male broilers (n = 525) were allocated to five experimental treatments for 42 days. Each treatment had three replicates of 35 broilers each. Depending on the time-frame of sequential or continuous addition in the basal diet (BD) of the probiotics (108 CFU/kg BD) and phytogenics (125 mg/kg BD), experimental treatments were: control (no additions, Days 1–42); PE1, probiotic Days 1–14 and phytogenic Days 15–42; PE2, probiotic Days 1–28 and phytogenic Days 29–42; PE3, probiotic and phytogenic continuously (Days 1–42); and A (2.5 mg avilamycin/kg diet, Days 1–42). There was no loss of probiotic viability upon mixing with the phytogenic for up to 7 days. Overall bodyweight gain was higher (P = 0.025) in the control and PE1 than PE2 and PE3, whereas Treatment A was intermediate and not different from the rest. Overall feed intake in the control was the highest (P = 0.003). Treatments PE1, PE2 and PE3 had better (P = 0.004) overall feed conversion ratio (FCR) than the control. The FCR in PE1 and PE3 did not differ from A, which had the best FCR. Mortality did not differ among treatments. Nutrient digestibility and caecal microbiota composition did not differ among treatments. However, differences (P ≤ 0.05) in caecal VFA pattern were noted, with the control having the lowest acetate molar ratio as well as the highest sum of valeric, hexanoic and heptanoic acids. Plasma TAC in the control was lower than in PE3, PE1 and PE2 at Day 14 (P < 0.001) and PE1 (P = 0.003) at Day 42. The concept of sequential or throughout probiotic and phytogenic administration showed promising results regarding feed efficiency and plasma TAC.

scholarly journals Inventory of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae in France as Assessed by a Multicenter Study

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
F. Robin ◽  
R. Beyrouthy ◽  
S. Bonacorsi ◽  
N. Aissa ◽  
L. Bret ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Multicenter Study ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Clinical Samples ◽  
Content Type ◽  
Extended Spectrum ◽  
Plasmid Analysis ◽  
Encoding Genes ◽  
Plasmid Replicons

ABSTRACT The objective of this study was to perform an inventory of the extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae isolates responsible for infections in French hospitals and to assess the mechanisms associated with ESBL diffusion. A total of 200 nonredundant ESBL-producing Enterobacteriaceae strains isolated from clinical samples were collected during a multicenter study performed in 18 representative French hospitals. Antibiotic resistance genes were identified by PCR and sequencing experiments. The clonal relatedness between isolates was investigated by the use of the DiversiLab system. ESBL-encoding plasmids were compared by PCR-based replicon typing and plasmid multilocus sequence typing. CTX-M-15, CTX-M-1, CTX-M-14, and SHV-12 were the most prevalent ESBLs (8% to 46.5%). The three CTX-M-type EBSLs were significantly observed in Escherichia coli (37.1%, 24.2%, and 21.8%, respectively), and CTX-M-15 was the predominant ESBL in Klebsiella pneumoniae (81.1%). SHV-12 was associated with ESBL-encoding Enterobacter cloacae strains (37.9%). qnrB, aac(6′)-Ib-cr, and aac(3)-II genes were the main plasmid-mediated resistance genes, with prevalences ranging between 19.5% and 45% according to the ESBL results. Molecular typing did not identify wide clonal diffusion. Plasmid analysis suggested the diffusion of low numbers of ESBL-encoding plasmids, especially in K. pneumoniae and E. cloacae. However, the ESBL-encoding genes were observed in different plasmid replicons according to the bacterial species. The prevalences of ESBL subtypes differ according to the Enterobacteriaceae species. Plasmid spread is a key determinant of this epidemiology, and the link observed between the ESBL-encoding plasmids and the bacterial host explains the differences observed in the Enterobacteriaceae species.

scholarly journals Monoclonal Antibodies as an Antibacterial Approach Against Bacterial Pathogens

Antibiotics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 155 ◽  
Author(s):  
Daniel V. Zurawski ◽  
Molly K. McLendon
Keyword(s):  
Monoclonal Antibodies ◽  
Bacterial Infection ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Potential Game ◽  
Virulence Proteins ◽  
Root Cause ◽  
Success Stories ◽  
In The Beginning ◽  
Patient Use

In the beginning of the 21st century, the frequency of antimicrobial resistance (AMR) has reached an apex, where even 4th and 5th generation antibiotics are becoming useless in clinical settings. In turn, patients are suffering from once-curable infections, with increases in morbidity and mortality. The root cause of many of these infections are the ESKAPEE pathogens (Enterococcus species, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli), which thrive in the nosocomial environment and are the bacterial species that have seen the largest rise in the acquisition of antibiotic resistance genes. While traditional small-molecule development still dominates the antibacterial landscape for solutions to AMR, some researchers are now turning to biological approaches as potential game changers. Monoclonal antibodies (mAbs)—more specifically, human monoclonal antibodies (Hu-mAbs)—have been highly pursued in the anti-cancer, autoimmune, and antiviral fields with many success stories, but antibody development for bacterial infection is still just scratching the surface. The untapped potential for Hu-mAbs to be used as a prophylactic or therapeutic treatment for bacterial infection is exciting, as these biologics do not have the same toxicity hurdles of small molecules, could have less resistance as they often target virulence proteins rather than proteins required for survival, and are narrow spectrum (targeting just one pathogenic species), therefore avoiding the disruption of the microbiome. This mini-review will highlight the current antibacterial mAbs approved for patient use, the success stories for mAb development, and new Hu-mAb products in the antibacterial pipeline.

scholarly journals Potential of fascaplysin and palauolide from Fascaplysinopsis cf reticulata to reduce the risk of bacterial infection in fish farming

2019 ◽  
Vol 22 (1) ◽  
Author(s):  
Tepoerau Mai ◽  
Jordan Toullec ◽  
Simon Van Wynsberge ◽  
Marc Besson ◽  
Stephanie Soulet ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Poecilia Reticulata ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Fish Farming ◽  
Homoserine Lactone ◽  
French Polynesia ◽  
Future Research ◽  
Quorum Sensing Inhibitors ◽  
First Time

AbstractMarine natural products isolated from the sponge Fascaplysinopsis cf reticulata, in French Polynesia, were investigated as an alternative to antibiotics to control pathogens in aquaculture. The overuse of antibiotics in aquaculture is largely considered to be an environmental pollution, because it supports the transfer of antibiotic resistance genes within the aquatic environment. One environmentally friendly alternative to antibiotics is the use of quorum sensing inhibitors (QSIs). Quorum sensing (QS) is a regulatory mechanism in bacteria which control virulence factors through the secretion of autoinducers (AIs), such as acyl-homoserine lactone (AHL) in gram-negative bacteria. Vibrio harveyi QS is controlled through three parallel pathways: HAI-1, AI-2, and CAI-1. Bioassay-guided purification of F. cf reticulata extract was conducted on two bacterial species, i.e., Tenacibaculum maritimum and V. harveyi for antibiotic and QS inhibition bioactivities. Toxicity bioassay of fractions was also evaluated on the freshwater fish Poecilia reticulata and the marine fish Acanthurus triostegus. Cyclohexanic and dichloromethane fractions of F. cf reticulata exhibited QS inhibition on V. harveyi and antibiotic bioactivities on V. harveyi and T. maritimum, respectively. Palauolide (1) and fascaplysin (2) were purified as major molecules from the cyclohexanic and dichloromethane fractions, respectively. Palauolide inhibited QS of V. harveyi through HAI-1 QS pathway at 50 μg ml–1 (26 μM), while fascaplysin affected the bacterial growth of V. harveyi (50 μg ml–1) and T. maritimum (0.25 μg). The toxicity of fascaplysin-enriched fraction (FEF) was evaluated and exhibited a toxic effect against fish at 50 μg ml–1. This study demonstrated for the first time the QSI potential of palauolide (1). Future research may assess the toxicity of both the cyclohexanic fraction of the sponge and palauolide (1) on fish, to confirm their potential as alternative to antibiotics in fish farming.

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

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 748 ◽  
Author(s):  
Jin-Young Lee ◽  
Mohamed Mannaa ◽  
Yunkyung Kim ◽  
Jehun Kim ◽  
Geun-Tae Kim ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Stool Samples ◽  
Gut Microbiota Composition

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

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