Rafat Al Jassim

Functional Gene Analysis Suggests Different Acetogen Populations in the Bovine Rumen and Tammar Wallaby Forestomach

ABSTRACT Reductive acetogenesis via the acetyl coenzyme A (acetyl-CoA) pathway is an alternative hydrogen sink to methanogenesis in the rumen. Functional gene-based analysis is the ideal approach for investigating organisms capable of this metabolism (acetogens). However, existing tools targeting the formyltetrahydrofolate synthetase gene (fhs) are compromised by lack of specificity due to the involvement of formyltetrahydrofolate synthetase (FTHFS) in other pathways. Acetyl-CoA synthase (ACS) is unique to the acetyl-CoA pathway and, in the present study, acetyl-CoA synthase genes (acsB) were recovered from a range of acetogens to facilitate the design of acsB-specific PCR primers. fhs and acsB libraries were used to examine acetogen diversity in the bovine rumen and forestomach of the tammar wallaby (Macropus eugenii), a native Australian marsupial demonstrating foregut fermentation analogous to rumen fermentation but resulting in lower methane emissions. Novel, deduced amino acid sequences of acsB and fhs affiliated with the Lachnospiraceae in both ecosystems and the Ruminococcaeae/Blautia group in the rumen. FTHFS sequences that probably originated from nonacetogens were identified by low “homoacetogen similarity” scores based on analysis of FTHFS residues, and comprised a large proportion of FTHFS sequences from the tammar wallaby forestomach. A diversity of FTHFS and ACS sequences in both ecosystems clustered between the Lachnospiraceae and Clostridiaceae acetogens but without close sequences from cultured isolates. These sequences probably originated from novel acetogens. The community structures of the acsB and fhs libraries from the rumen and the tammar wallaby forestomach were different (LIBSHUFF, P < 0.001), and these differences may have significance for overall hydrogenotrophy in both ecosystems.

The bacterial community of the horse gastrointestinal tract and its relation to fermentative acidosis, laminitis, colic, and stomach ulcers.

The gastrointestinal tract of the horse has unique characteristics that make it well suited for the ingestion and utilization of roughage. The horse is considered a simple-stomached herbivore and is classed as a hindgut fermenter. The upper segments of the gastrointestinal tract resemble those of a typical simple-stomached animal. The lower have undergone modification to become voluminous and host to a large number of microbial populations similar to those of the compartmental stomach of ruminant animals. The main advantage of this arrangement is the ability of the horse to extract valuable nutrients from the diet before digesta reaches the hindgut where the rigid structural components that resisted enzymatic digestion at the small intestinal level undergo extensive fermentation processes.

Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius)

The molecular diversity of the foregut bacterial community in the dromedary camel (Camelus dromedarius) in Central Australia was investigated through comparative analyses of 16S rRNA gene sequences prepared from the foregut contents of 12 adult feral camels fed on native vegetation. A total of 267 full-length 16S rRNA gene clones were examined, with 151 operational taxonomic units (OTUs) identified at a 99% species-level identity cut-off criterion. The prediction of actual diversity in the foregut of the dromedary camel using the Chaol approach was 238 OTUs, while the richness and evenness of the diversity estimated using Shannon index was 4.84. The majority of bacteria in the current study were affiliated with the bacterial phylum Firmicutes (67% of total clones) and were related to the classes Clostridia, Bacilli and Mollicutes, followed by the Bacteroidetes (25%) that were mostly represented by the family Prevotellaceae. The remaining phyla were represented by Actinobacteria, Chloroflexi, Cynophyta, Lentisphaerae, Planctomycetes, Proteobacteria and Sphirochaetes. Moreover, 11 clones of cultivated bacteria were identified as Brevundimonas sp., Butyrivibrio fibrisolvens, Prevotella sp. and Ruminococcus flavefaciens. The novelty in this foregut environment is remarkable where 97% of the OTUs were distantly related to any known sequence in the public database.

Antimicrobial activity of essential oils and five terpenoid compounds against Campylobacter jejuni in pure and mixed culture experiments

The aim of this study was to examine the antimicrobial potential of three essential oils (EOs: tea tree oil, lemon myrtle oil and Leptospermum oil), five terpenoid compounds (α-bisabolol, α-terpinene, cineole, nerolidol and terpinen-4-ol) and polyphenol against two strains of Campylobacter jejuni (ACM 3393 and the poultry isolate C338), Campylobacter coli and other Gram negative and Gram positive bacteria. Different formulations of neem oil (Azadirachta indica) with these compounds were also tested for synergistic interaction against all organisms. Antimicrobial activity was determined by the use of disc diffusion and broth dilution assays. All EOs tested were found to have strong antimicrobial activity against Campylobacter spp. with inhibitory concentrations in the range 0.001-1% (v/v). Among the single compounds, terpinen-4-ol showed the highest activity against Campylobacter spp. and other reference strains. Based on the antimicrobial activity and potential commerciality of these agents, lemon myrtle oil, α-tops (α-terpineol+cineole+terpinen-4-ol) and terpinen-4-ol were also evaluated using an in vitro fermentation technique to test antimicrobial activity towards C. jejuni in the microbiota from the chicken-caecum. EO compounds (terpinen-4-ol and α-tops) were antimicrobial towards C. jejuni at high doses (0.05%) without altering the fermentation profile. EOs and terpenoid compounds can have strong anti-Campylobacter activity without adversely affecting the fermentation potential of the chicken-caeca microbiota. EOs and their active compounds may have the potential to control C. jejuni colonisation and abundance in poultry.

Screening of Australian plants for antimicrobial activity against Campylobacter jejuni.

Campylobacter jejuni is the most common cause of acute enteritis in humans, with symptoms such as diarrhoea, fever and abdominal cramps. In this study, 115 extracts from 109 Australian plant species were investigated for their antimicrobial activities against two C. jejuni strains using an in vitro broth microdilution assay. Among the plants tested, 107 (93%) extracts showed activity at a concentration between 32 and 1024 µg/mL against at least one C. jejuni strain. Seventeen plant extracts were selected for further testing against another six C. jejuni strains, as well as Campylobacter coli, Escherichia coli, Salmonella typhimurium, Bacillus cereus, Proteus mirabilis and Enterococcus faecalis. The extract from Eucalyptus occidentalis demonstrated the highest antimicrobial activity, with an inhibitory concentration of 32 µg/mL against C. jejuni and B. cereus. This study has shown that extracts of selected Australian plants possess antimicrobial activity against C. jejuni and thus may have application in the control of this organism in live poultry and retail poultry products. Copyright

Staphylococcus aureus ST398 detected in pigs in Australia

Alackoftargeted surveillance means that the presence of MRSA inAustralian food-producing animals may have gone undetected.We report here the first detection of MRSA in Australian pigs, themolecularcharacteristicsoftherecoveredisolatesandtheimpacton our understanding of the global epidemiology of this prioritypathogen.Nasal swabs were collected from 324 pigs in five commercialherds and one feral herd between January 2009 and October2010. Swabs were obtained from herds in Western Australia(feral pigs, Herd 1), Queensland (Herd 2), Victoria (Herd 3) andNew South Wales (Herds 4–6). The collection of nasal samplesfrom pigs was approved by the Animal Ethics Committee of theElizabeth Macarthur Agricultural Institute, Menangle, New SouthWales (reference M10/06). Swabs were suspended in 2 mL ofbrain heart infusion broth (Oxoid, Adelaide, Australia) containing20% (v/v) glycerol and stored at 2808C. Pools containing 100 mLeach of five nasal samples were prepared in 2 mL of Mueller–Hintonbroth(Oxoid)containing6.5%NaClandenrichedovernightat 358C. Each pool was analysed by PCR for markers indicative ofMRSA (femB and mecA).

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.

Cellulolytic Bacteria in the Foregut of the Dromedary Camel (Camelus dromedarius)

ABSTRACT Foregut digesta from five feral dromedary camels were inoculated into three different enrichment media: cotton thread, filter paper, and neutral detergent fiber. A total of 283 16S rRNA gene sequences were assigned to 33 operational taxonomic units by using 99% species-level identity. LIBSHUFF revealed significant differences in the community composition across all three libraries.

Determination of hepatotoxic indospicine in Australian camel meat by ultra-performance liquid chromatography-tandem mass spectrometry.

Indospicine is a hepatotoxic amino acid found in Indigofera plant spp. and is unusual in that it is not incorporated into protein but accumulates as the free amino acid in the tissues (including muscle) of animals consuming these plants. Dogs are particularly sensitive to indospicine, and secondary poisoning of dogs has occurred from the ingestion of indospicine-contaminated horse meat and more recently camel meat. In central Australia, feral camels are known to consume native Indigofera species, but the prevalence of indospicine residues in their tissues has not previously been investigated. In this study, a method was developed and validated with the use of ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to determine the level of indospicine in camel meat samples using isotopically labeled indospicine as an internal standard. UPLC-MS/MS analysis showed that the method is reproducible, with high recovery efficiency and a quantitation limit of 0.1 mg/kg. Camel meat samples from the Simpson Desert were largely contaminated (≈50%) by indospicine with levels up to 3.73 mg/kg (fresh weight) determined. However, the majority of samples (95%) contained less than 1 mg/kg indospicine.

Effects of feeding plant-derived agents on the colonization of Campylobacter jejuni in broiler chickens

The aim of this work was to test the potential use of plant-derived extracts and compounds to control Campylobacter jejuni in broiler chickens. Over a 7-wk feeding period, birds were fed a commercial diet with or without plant extracts (Acacia decurrens, Eremophila glabra), essential oil [lemon myrtle oil (LMO)], plant secondary compounds [terpinene-4-ol and α-tops (including α-terpineol, cineole, and terpinene-4-ol)], and the antibiotic virginiamycin. Traditional culture and real-time quantitative PCR techniques were used to enumerate the numbers of C. jejuni in chicken fecal and cecal samples. In addition, BW and feed intake were recorded weekly for the calculation of BW gain and feed conversion ratio. The mean log10 counts of C. jejuni were similar (P > 0.05) across treatments. However, significantly lower levels of fecal Campylobacter counts (P < 0.05) were recorded at d 41 for the α-tops treatment by culture methods. No differences (P > 0.05) in BW gain were obtained for dietary supplementation, except for the E. glabra extract, which had a negative impact (P < 0.001) on BW, resulting in sporadic death. Results from this study suggest that supplemental natural compounds used in the current study did not reduce the shedding of C. jejuni to desired levels.