Untreated surface waters can be contaminated with a variety of bacteria, including Escherichia coli, some of which can be pathogenic for both humans and animals. Therefore, such waters need to be ...treated before their use in dairy operations to mitigate risks to dairy cow health and milk safety. To understand the molecular ecology of E. coli, this study aimed to assess antimicrobial resistance (AMR) in E. coli recovered from untreated surface water sources of dairy farms. Untreated surface water samples (n = 240) from 15 dairy farms were collected and processed to isolate E. coli. A total of 234 E. coli isolates were obtained and further characterized for their serotypes and antimicrobial susceptibility. Of the 234 isolates, 71.4% were pan‐susceptible, 23.5% were resistant to one or two antimicrobial classes, and 5.1% were resistant to three or more antimicrobial classes. Whole genome sequence analysis of 11 selected multidrug‐resistant isolates revealed AMR genes including blaCMY‐2 and blaCTX‐M‐1 that confer resistance to the critically important extended‐spectrum cephalosporins, as well as a variety of plasmids (mainly of the IncF replicon type) and class 1 integrons. Phylogenetic and comparative genome analysis revealed a genetic relationship between some of the sequenced E. coli and Shiga toxin‐producing E. coli O157:H7 (STEC), which warrants further investigation. This study shows that untreated surface water sources contain antimicrobial‐resistant E. coli, which may serve as a reservoir of AMR that could be disseminated through horizontal gene transfer. This is another reason why effective water treatment before usage should be routinely done on dairy farm operations.
Core Ideas
Surface water is a valuable input for livestock production.
Untreated surface water can be a source of antimicrobial‐resistant bacteria.
Multidrug‐resistant E. coli strains may facilitate spread of antimicrobial resistance (AMR).
Whole genome sequencing provides insight into the molecular ecology of E. coli from surface water.
This highlights the need to implement efficient water treatment units for dairy farms.
Abstract
Essential oils are potential antimicrobial alternatives and their applications in animal feeds are limited due to their fast absorption in the upper gastrointestinal tract. This study ...investigated the effects of encapsulated cinnamaldehyde (CIN) at 50 mg/kg or 100 mg/kg on the growth performance, organ weights, meat quality, intestinal morphology, jejunal gene expression, nutrient digestibility, and ileal and cecal microbiota. A total of 320 male day-old broiler Cobb-500 chicks were randomly allocated to four treatments with eight pens per treatment (10 birds per pen): 1) basal diet (negative control, NC); 2) basal diet supplemented with 30 mg/kg avilamycin premix (positive control, PC); 3) basal diet with 50 mg/kg encapsulated CIN (EOL); 4) basal diet with 100 mg/kg encapsulated CIN (EOH). Despite birds fed EOH tended to increase (P = 0.05) meat pH at 24 h, all pH values were normal. Similar to PC group, meats from birds fed EOL and EOH showed a reduced (P < 0.05) Warner–Bratzler force shear (WBFS) compared to the NC group. The highest villus to crypt ratios (VH/CD; P < 0.05) were observed in broilers fed either EOL or EOH, with an average of 14.67% and 15.13% in the duodenum and 15.13% and 13.58% in the jejunum, respectively. For jejunal gene expressions, only six out of the 11 studied genes showed statistically significant differences among the dietary treatments. Gene expressions of cationic amino acid transporter 1 (CAT-1) and neutral amino acid transporter 1 (B0AT-1) were upregulated in EOH-fed birds compared to PC and NC-fed birds (P < 0.05), respectively; while the expression of proliferating cell nuclear antigen (PCNA) was downregulated in EOL-fed birds when compared to NC birds (P < 0.05). Nonetheless, the expressions of cadherin 1 (CDH-1), zonula occludens 1 (ZO-1), and maltase-glucoamylase (MG) were all upregulated (P < 0.05) in EOH-fed birds compared to PC-fed birds. The apparent ileal digestibility (AID) of dry matter, crude protein, crude fat and of all 18 tested amino acids increased in EOL-fed birds (P < 0.01). Additionally, relative abundances (%) of ileal Proteobacteria decreased, while ileal and cecal Lactobacillus increased in EOH-fed birds (P < 0.05). In conclusion, dietary encapsulated CIN improved meat quality and gut health by reducing meat WBFS, increasing VH/CD in intestines, jejunal gene expressions, AID of nutrients and beneficial ileal and cecal microbiota composition.
Necrotic enteritis (NE) is an economically important disease of poultry caused by certain
type A strains. The NetB toxin plays a critical role in the pathogenesis of NE. We previously demonstrated ...that
is located within a 42 kb plasmid-encoded pathogenicity locus (NELoc-1), which also encodes 36 additional genes. Although NetB clearly plays a role in pathogenesis, the involvement of the other NELoc-1 genes has not yet been established. The current study was to provide experimental evidence to confirm the involvement of these genes in NE pathogenesis.
The present study has characterized a virulent
strain (CP1) that has spontaneously lost the NELoc-1-encoding plasmid, pCP1netB. When assessed for cytotoxicity on Leghorn Male Hepatoma (LMH) cells, the culture supernatant of the pCP1netB-deficient CP1 variant (CP1ΔpCP1netB) demonstrated significantly reduced cytotoxicity compared to the wild-type. In addition, CP1ΔpCP1netB was unable to cause intestinal lesions in chickens in a NE disease model. When
alone was introduced into CP1ΔpCP1netB, in vitro cytotoxicity was restored to the wild-type level; however, it did not completely restore virulence when used to challenge broiler chickens mean lesion score of 0.71 compared to 3.23 in the wild type control group (n = 14).
The results of this study suggest that other genes present in NELoc-1, in addition to
, are required for full virulence in the chicken challenge model.
•Clostridium perfringens isolates that cause avian necrotic enteritis have a large pathogenicity locus NELoc-1.•Mutation of the dgc and pde genes on NELoc-1 completely attenuated the ability of ...strain CP1 to cause necrotic enteritis.•Complementation with the relevant gene fully restored virulence.•NetB production was unaffected in the two mutants.•c-di-GMP signaling is thus important in the pathogenesis of necrotic enteritis in chickens.
Necrotic enteritis (NE) caused by netB-positive strains of Clostridium perfringens is an important disease of intensively-reared broiler chickens. It is widely controlled by antibiotic use, but this practice that has come under increasing scrutiny and alternative approaches are required. As part of the search for alternative approaches over the last decade, advances have been made in understanding its pathogenesis but much remains to be understood and applied to the control of NE. The objective of this work was to assess the effect on virulence of mutation of the cyclic-di-GMP signaling genes present on the large pathogenicity locus (NELoc-1) in the tcp-encoding conjugative virulence plasmid, pNetB. For this purpose, the diguanylate cyclase (dgc) and phosphodiesterase (pde) genes were individually insertionally inactivated and the two mutants were subsequently complemented with their respective genes. Southern blotting showed that a single gene insertion was present. Mutation of either gene resulted in almost total attenuation of the mutants to cause NE in experimentally-infected broiler chickens, which was fully restored in each case by complementation of the respective mutated gene. Production of NetB-associated cytotoxicity for Leghorn male hepatoma (LMH) cells was unaffected in mutants. We conclude that the cyclic-di-GMP signaling system is important in controlling virulence in a NE C. perfringens strain and might be a target for control of the disease.
Scope
This study investigated the effects of cooked whole asparagus (ASP) versus its equivalent level of purified flavonoid glycoside, rutin (RUT), on dextran sodium sulfate (DSS)‐induced colitis and ...subsequent colitis recovery in mice.
Methods and results
C57BL/6 male mice were fed an AIN‐93G basal diet (BD), or BD supplemented with 2% cooked ASP or 0.025% RUT for 2 wks prior to and during colitis induction with 2% DSS in water for 7 days, followed by 5 days colitis recovery. In colitic mice, both ASP and RUT upregulated mediators of improved barrier integrity and enhanced mucosal injury repair (e.g. Muc1, IL‐22, Rho‐A, Rac1, and Reg3γ), increased the proportion of mouse survival, and improved disease activity index. RUT had the greatest effect in attenuating DSS‐induced colonic damage indicated by increased crypt and goblet cell restitution, reduced colonic myeloperoxidase, as well as attenuated DSS‐induced microbial dysbiosis (reduced Enterobacteriaceae and Bacteroides, and increased unassigned Clostridales, Oscillospira, Lactobacillus, and Bifidobacterium).
Conclusion
These findings demonstrate that dietary cooked ASP and its flavonoid glycoside, RUT, may be useful in attenuating colitis severity by modulating the colonic microenvironment resulting in reduced colonic inflammation, promotion of colonic mucosal injury repair, and attenuation of colitis‐associated microbial dysbiosis.
Cooked asparagus officinalis (ASP) and its purified bioactive, rutin (RUT), are studied for their ability to modulate the colonic microenvironment and reduce colitis in C57Bl/6 mice. Both diets reduce colonic inflammation, promote injury repair, and attenuate colitis‐associated microbial dysbiosis. RUT is more effective than ASP (whole food)
Abstract only
Fiber‐rich dietary pulses, such as common beans (
Phaseolus vulgaris
) have the potential to modify the colonic microenvironment (microbiota and host epithelial barrier) which can ...mitigate the severity of gut‐associated pathologies. Obesity is associated with impairments in the mucosal barrier (leaky gut) and specific changes in the abundance of bacteria communities within the gut microbiota. The objective was to assess the gut health promoting effects of 20% cooked navy bean flour supplementation in both the lean healthy and obese states. Two studies were conducted wherein male C57BL/6 mice were fed either a low fat control (LF, 10% fat as kcal) or an isocaloric bean supplemented diet (LF+B) for 3 weeks (
Study 1: lean healthy
), or a high fat diet (HF, 60% fat as kcal) or isocaloric bean supplemented (HF+B) diet for 12 weeks (
Study 2: diet induced obesity
). In lean mice, using fecal 16S rRNA sequencing, LF+B altered the abundance of critical gut microbial families including increased abundance of S24–7 (1.5‐fold) and Prevotellaceae (71‐fold) and decreased abundance of Peptococcaceae (3.7‐fold), Streptococcaceae (8.4‐fold), Clostridiaceae (12‐fold), Rikenellaceae (2.5‐fold) and Porphyromonadaceae (2.5‐fold) versus LF. These changes were associated with increased microbial activity (i.e, short chain fatty acid (SCFA) production) and colonic tissue expression of the SCFA receptors
GPR41
,
43
and
109a
. LF+B improved gut barrier integrity and function by increasing i) mucus production, ii) anti‐microbial defenses, iii) tight junction protein expression, and iv) reducing serum lipopolysaccharide levels. These beneficial effects were sustained in obesity wherein HF+B fed mice exhibited improvements in both gut microbiota activity and community structure and aspects of the obese phenotype. Specifically, fecal abundance of
Akkermansia muciniphila
, whose abundance is inversely related to the severity of the obese phenotype, was increased in the HF+B group versus HF by 20‐fold, which was associated with a reduction in visceral adipose mRNA expression of the inflammatory mediators
MCP‐1
and
IL‐6
and increased expression of
adiponectin
. Colon epithelial barrier integrity was improved in the HF+B group versus HF, as evidenced by increased mRNA expression of tight junction components (
ZO‐1, occludin, JAM‐A
and
claudin‐2
) and functionally by reduced serum FITC‐dextran concentration in an in vivo gut permeability test. Additionally, evidence of an enhanced mucus barrier and anti‐microbial defence was apparent in the HF+B group versus HF based on increased goblet cell number and upregulated expression of
Muc1‐3
and
Reg3
γ, respectively. In conclusion, bean supplementation enhanced gut barrier integrity and exerted a beneficial colon‐function priming effect that helps mitigate the severity of the obese phenotype.
Support or Funding Information
ORF, AAFC Pulse‐Cluster
Dietary impacts on the colonic microbiota can play an important role in maintaining gut health, however direct evaluation of these effects is challenging in the complex intestinal environment of the ...host. In vitro models of digestion allow for rigorous standardization without the ethical considerations that accompany human or animal studies. In the current study, a combined in vitro model of upper gut digestion and lower gut fermentation (RoboGut system) was used to assess the effects of lentils on the composition and activity of defined microbial communities derived from individual human donors. Microbial communities were developed from two healthy donors (HD5 and HD6) by exhaustive culturing of donor stool on different media, resulting in 63 and 58 isolates, respectively. Fermentation vessels were seeded in duplicate with each community and cultured for one week each in basal media, followed by lentil-supplemented media, and finally basal media again. The microbial community structure was examined at regular intervals by 16S rRNA gene sequencing and QIIME analysis. Principal coordinate analysis (PCoA) of weighted UniFrac distances revealed the community compositions of both HD5 and HD6 shifted within 2 days of lentil supplementation, but quickly reverted back to their original states after removal of lentil. Specifically, the abundance of 27 and 20 community members from HD5 and HD6, respectively, were significantly altered by lentil supplementation, as determined by LEfSe analysis, whereas no significant differences in taxa abundances were observed in control vessels without lentil supplementation. Eighteen and 15 respective species within HD5 and HD6 increased in abundance in response to lentil supplementation, six of which were common to both communities: Blautia producta, Collinsella aerofaciens, Bacteroides vulgatus, Eubacterium limosum, Escherichia coli and Eubacterium eligens. A significant increase in production of the short-chain fatty acid (SCFA) acetate was also observed during lentil-supplementation, compared to pre-lentil. This work establishes a novel standardized in vitro model for studying the effects of whole foods on the human gut microbiota. The results indicate that lentil diets can cause a non-permanent shift in key constituents of the human gut microbiota, thereby altering production of SCFAs.
Abstract only
Dietary impacts on the colonic microenvironment (microbiota and mucosal barrier) can play an important role in modulating gut‐associated inflammatory diseases, such as inflammatory ...bowel disease (IBD).Pulses, such as common beans and chickpeas, are rich sources of gut health promoting bioactives, including non‐digestible fermentable carbohydrates and phenolics, however, research demonstrating whole pulse effects on the colonic microenvironment and subsequent inflammatory pathologies, are lacking. Our objectives were to determine the effects of cooked bean and chickpea diets on critical aspects of colon health (microbiota activity and community structure, and colonic epithelial barrier integrity and function) and subsequent effects on disease severity following colitis‐associated mucosal injury. In study 1, male C57Bl/6 mice were fed a 20% cooked black bean flour supplemented diet (BB) or an isocaloric control diet (CON) for 3 weeks, followed by exposure to dextran sodium sulphate (DSS, 2% w/v, 5d) to test the ability of BB to prime the colon and attenuate the severity of colitis‐induced damage mimicking IBD. In study 2, a similar study design was used except mice were fed CON or diet supplemented with 20% cooked chickpeas.
Prior to DSS‐exposure (healthy mice; n=10/diet), BB diet increased i) colon crypt height, goblet cell number, and mucus production, ii) mRNA expression of MUC1‐3, RELMβ, REG3γ, IgA, occludin and JAM‐A, and iii) reduced serum LPS levels compared to CON, indicative of enhanced antimicrobial defense and gut barrier integrity. Furthermore, compared to CON, BB consumption i) increased microbial‐derived cecal short chain fatty acids (SCFAs) acetate, butyrate, and propionate, and ii) altered the colonic microbial community structure (increased Prevotellaceae, Porphyromonadaceae, and S24‐7 and reduced Rikenellaceae, Lachnospiraceae, Streptococcaceae, Erysipelotrichaceae, Peptococcaceae, and Peptostreptococcaceae), as measured by fecal 16S rRNA sequencing. During colitis (n=10/diet), BB‐fed mice had increased colonic mRNA expression of microbial‐responsive and epithelial barrier integrity promoting genes (MUC1‐3, RELMβ, and TFF3) and reduced colonic pro‐inflammatory mediator production (IL‐1β, IL‐6, IFN‐γ, and TNF‐α). Similar effects of chickpea supplementation were observed in healthy (enhanced mucosal barrier and microbial activity and altered microbial community structure) and colitic mice (reduced disease severity).
In conclusion, pulse supplementation resulted in an improved colonic microenvironment as demonstrated by beneficial changes to the microbial community structure and activity, and increased colonic mucosal barrier integrity. This led to an attenuation of colonic damage following DSS‐induced colitis. Therefore, regular consumption of pulse foods may beneficially prime the colonic microenvironment to better respond to inflammatory insults which can mitigate development and severity of inflammation‐associated colonic diseases.
Support or Funding Information
ORF; AAFC‐Pulse Canada
Agricultural soils constitute highly diverse ecosystems with very rich bacterial populations. Recent studies employing next-generation sequencing techniques have begun to explore the dynamics of ...bacterial species of such soils and utilized metagenomics approaches to understand how the diversity in soil microorganisms is affected or modified by agricultural practices. Understanding any microorganism's environmental adaptability in the genomic era starts by fully appreciating their encoding genome. Here, we report the draft genome sequences of three Devosia species based on three type strains that originated from soil samples: D. insulae strain DS-56, D. limi strain DSM17137, and D. soli strain GH2-10.
Here, we present the draft genome sequence of
strain A47 with a length of 4,878,242 bp, which contains 4,357 putative protein coding genes, including 270 unique genes. This work is expected to assist ...in obtaining novel gene(s) that code for deoxynivalenol (DON) de-epoxidation enzyme(s).
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