Christina Diane Moon

AgResearch · Resilient Agriculture

Xylanibacter ruminicola is an abundant rumen bacterium that produces propionate in a cobalamin (vitamin B12)-dependent manner via the succinate pathway. However, the extent to which this occurs across ruminal Xylanibacter and closely related bacteria, and the effect of cobalamin supplementation on the expression of propionate pathway genes and enzy...

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF...

Epichloë (Clavicipitaceae) is a genus of filamentous fungal endophytes that have co-evolved with cool-season grasses with which they form perpetual, symbiotic associations. In natural ecosystems Epichloë endophytes have implications for species diversity, food web structures, and fundamental ecological processes. In many managed pastoral systems, s...

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen mycobiome by examining 206 samples from 15 animal species, 15 countries and six continents. The rumen mycobio...

Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56...

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order 'Christensenellales', were phylogenetically and phenotypically characterized. These strains, designated R-7T and WTE2008T, shared 98.6-99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T...

Asexual Epichloë are endophytic fungi that form mutualistic symbioses with cool-season grasses, conferring to their hosts protection against biotic and abiotic stresses. Symbioses are maintained between grass generations as hyphae are vertically transmitted from parent to progeny plants through seed. However, endophyte transmission to the seed is a...

The aim of this review was to summarise the available literature on the effects of consuming raw red meat diets on the gastrointestinal microbiome of the cat and dog. In recent years, feeding raw meat diets to cat and dogs has increased, in part associated with trends in human nutrition for “natural” and “species-appropriate” diets. These diets ran...

Members of the Clostridiales R-7 group are abundant bacterial residents of the rumen microbiome; however, they are poorly characterized. We report the complete genome sequences of three members of the R-7 group, FE2010, FE2011, and XBB3002, isolated from the ruminal contents of pasture-grazed dairy cows in New Zealand.

This paper reports relationships between fatty acids (FAs) and intramuscular fat (IMF)% in M. longissimus lumborum samples from 108 pasture-fed ewe lambs. Samples ranged in IMF from 1 to 6%. Relationships between %FA with total IMF% were mainly linear with percentages of saturated and monounsaturated FAs (MUFA), including trans-FAs, increasing and...

Background The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, th...

Anthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that include...

Palatability of meat is known to be affected by intramuscular fat (IMF), but the effect in relatively low-fat New Zealand lamb is unknown. This study evaluated the eating quality of 108 loins (M. longissimus lumborum) from a single flock of ewe-lambs. Loins ranged from 1.09–5.68% IMF and were stratified into 6 groups: 1.65, 2.12, 2.65, 3.20, 3.58 a...

Agriculture plays a major role in New Zealand’s economy, with ruminant products contributing about one third of total export earnings. Ruminants produce methane, a major greenhouse gas that is a by-product of feed fermentation by the complex rumen microbial community. Several strategies are being explored to reduce methane yields from ruminants. Of...

The global spread of multidrug resistant enterobacteria warrants new strategies to combat these pathogens. One possible approach is reconsideration of “old” antimicrobials which remain effective after decades of use. Synthetic 5-nitrofurans such as furazolidone, nitrofurantoin and nitrofurazone, are such a class of antimicrobial drugs. Recent epide...

Endophytic Epichloë species form symbiotic associations with temperate grasses (Poaceae subfamily Poöideae). These symbionts are critical constituents of both natural grass ecosystems and cultivated agricultural grasslands providing improved persistence and production by protecting against biotic and abiotic stresses. The ecological significance of...

Vertical transmission of symbiotic Epichloë endophytes from host grasses into progeny seed is the primary mechanism by which the next generation of plants is colonized. This process is often imperfect, resulting in endophyte-free seedlings which may have poor ecological fitness if the endophyte confers protective benefits to its host. In this study...

In humans, aging is associated with changes in the gastrointestinal microbiota; these changes may contribute to the age-related increase in incidence of many chronic diseases, including Type 2 diabetes. The life expectancies of cats are increasing, and they are also exhibiting the same types of diseases. While there are some studies investigating t...

R codes for dataset intergration.

R codes for microbial analysis.

Interests in the impact of the gastrointestinal microbiota on health and wellbeing have extended from humans to that of companion animals. While relatively fewer studies to date have examined canine and feline gut microbiomes, analysis of the metagenomic DNA from fecal communities using next‐generation sequencing technologies have provided insights...

Background Many bacteria are facultative anaerobes, and can proliferate in both anoxic and oxic environments. Under anaerobic conditions, fermentation is the primary means of energy generation in contrast to respiration. Furthermore, the rates and spectra of spontaneous mutations that arise during anaerobic growth differ to those under aerobic grow...

Supplementary Tables

The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. The bacteria that attach to ingested plant matter within the rumen are thought to be responsible for initial fibre degradation. Most studies examining the ecology of this important microbiome only offer a ‘snapshot’ in time. We monitored the diver...

Bacterial taxa from the digesta-adherent fraction of rumen contents. Samples are identified by the month and animal they were sampled from. The first letter represents the month the sample was taken, M = May (Autumn), A = August (Winter), N = November (Spring), F = February (Summer) and L = May + 1yr (Autumn). The second letter represents the anima...

Barcoded primers for multiplex pyrosequencing PCR. Barcode sequences are highlighted in bold. Samples are identified by the month and animal they were sampled from. The first letter represents the month the sample was taken, M = May (Autumn), A = August (Winter), N = November (Spring), F = February (Summer) and L = May + 1yr (Autumn). The second le...

Scientific Reports 6 : Article number: 34668 10.1038/srep34668 ; published online: 23 November 2016 ; updated: 24 January 2017 The original version of this Article contained a typographical error in the title, where: “Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundan...

Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobi...

E. coli mutation rates calculated from fluctuation assays. (DOCX)

Spectra of BPSs amongst the aerobic and anaerobic lineages. (DOCX)

REL4536 IS element features and mutation rates. (DOCX)

Relative distribution of mutations within the macrodomains of E. coli. (DOCX)

Mutations detected amongst the aerobic and anaerobic lineages. (XLSX)

Expression values of E. coli REL4536 genes involved in DNA repair, replication and transposition. (DOCX)

Relative abundance of IS gene transcripts in aerobic and anaerobically grown cells. (DOCX)

Expression of genes involved in arginine biosynthesis. (DOCX)

Primers used to verify SV break points. (DOCX)

Significantly up-regulated genes, as a proportion of genes in the pathway, known to be involved in DNA repair and replication (classified by pathway). To identify significant expression, Benjamini-Hochberg adjusted p < 0.05 were used. Asterisk denotes a significant enrichment of the gene list under anaerobic conditions by Fisher’s exact test (*, p...

Genome re-sequencing reference-based mapping and de novo assembly statistics for MA clones. (XLSX)

Clockwise and counter-clockwise replichores of E. coli REL4536. (DOCX)

Cumulative distribution of mutations in the genomes of aerobic and anaerobic MA lineages. Shown are the relationships between cumulative mutations and chromosomal position for A) expected random distribution of mutations around the genome, B) BPSs, C) SVs, and D) indels. (TIF)

Comparison of mutation rates expressed per generation and per unit time. Shown are: Mean mutation rates of mutational classes expressed A) per nucleotide per generation, B) per nucleotide per day of growth, C) Conditional BPS rates expressed per nucleotide per generation and D) Conditional BPS rates expressed per nucleotide per day of growth. Error...

IS150 genome location. (DOCX)

Comparison of SV mutation rates. Shown are: A) and C) Mutation rates of different SV classes expressed per nucleotide per generation, and B) and D) Mutation rates of different SV classes expressed per nucleotide per day of growth. Error bars represent standard errors of the mean. * denotes p < 0.05 by Mann-Whitney U-test. (TIF)

Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and...

Glycoside hydrolase (GH) family 29 consists solely of α-l-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes....

We used a previously developed simulation model of a plant cell wall and its enzymatic degradation to compare the abilities of two hemicelluloses, glucuronoarabinoxylan (GAX) and xyloglucan (XG), to protect cellulose microfibrils (CMFs) from attack by cellulose-degrading enzymes. Additionally, we investigated the effect of XG abundance on the degra...

The rumen is the fermentative forestomach of ruminant animals, and is host to a wide range of anaerobic bacteria whose primary function is to facilitate forage degradation. Butyrivibrio and Pseudobutyrivibrio are closely related proteolytic and fibrolytic genera within the family Lachnospiraceae, and are commonly isolated from the rumens of animals...

Ruminal fibre degradation is mediated by a complex community of rumen microbes, and its efficiency is crucial for optimal dairy productivity. Enzymes produced by rumen microbes are primarily responsible for degrading the complex structural polysaccharides that comprise fibre in the plant cell walls of feed materials. Because rumen microbes have evo...

The rumen of dairy cattle can be thought of as a large, stable fermentation vat and as such it houses a large and diverse community of microorganisms. The bacterium Butyrivibrio proteoclasticus is a representative of a significant component of this microbial community. It is a xylan-degrading organism whose genome encodes a large number of open rea...

Complex microbial communities typically contain a large number of low abundance species, which collectively, comprise a considerable proportion of the community. This “rare biosphere” has been speculated to contain keystone species and act as a repository of genomic diversity to facilitate community adaptation. Many environmental microbes are curre...

Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be e...

Background In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecr...

The invention encompasses phage φmru including phage induction, phage particles, and the phage genome. Also encompassed are phage polypeptides, as well as polynucleotides which encode these polypeptides, expression vectors comprising these polynucleotides, and host cells comprising these vectors. The invention further encompasses compositions and m...

Butyrivibrio proteoclasticus is a significant component of the microbial population of the rumen of dairy cattle. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fibre-degrading enzymes. We have determined the three-dimensional structure of Est2A, an acetyl xylan esterase from B. proteoclasti...

The rumen bacterium Butyrivibrio proteoclasticus B316(T) has a 4.4-Mb genome composed of four replicons (approximately 3.55 Mb, 361, 302 and 186 kb). Mutagenesis of B316(T) was performed with the broad host-range conjugative transposon Tn916 to screen for functionally important characteristics. The insertion sites of 123 mutants containing a single...

Electron microscopy and light microscopy of B316. A, Transmission EM of B316 cells grown in liquid medium. B, Scanning EM of B316 cells growing on a clover leaf surface. C, Transmission EM of a thin section of a B316 cell showing the presence of pili. D, Transmission EM of a thin section of a B316 cell showing the presence of glycogen inclusions. E...

Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316(T) is a gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4 Mb genome consist...

Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provid...

Pseudomonads are able to form a variety of biofilms that colonize the air-liquid (A-L) interface of static liquid microcosms, and differ in matrix composition, strength, resilience and degrees of attachment to the microcosm walls. From Pseudomonas fluorescens SBW25, mutants have evolved during prolonged adaptation-evolution experiments which produc...

Bioprotective alkaloids produced by Epichloë and closely related asexual Neotyphodium fungal endophytes protect their grass hosts from insect and mammalian herbivory. One class of these compounds, known for antimammalian toxicity, is the indole-diterpenes. The LTM locus of Neotyphodium lolii (Lp19) and Epichloë festuce (Fl1), required for the biosy...

Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provid...

It is proposed that Clostridium proteoclasticum be reclassified as Butyrivibrio proteoclasticus comb. nov. on the basis of phylogenetic position, DNA G+C content and physiological traits. Phylogenetic analyses based on 16S rRNA gene sequences from an extensive range of taxa within clostridial rRNA subcluster XIVa grouped C. proteoclasticum together...

The development of high-throughput DNA sequencing techniques has enabled the sequencing of several hundred bacterial genomes. However, the major step towards understanding the molecular basis of an organism will be the determination of all gene functions in its genome. Current gene assignments by sequence homology generate numerous hints to putativ...