Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

This paper investigates the impact of lameness on milk yield. The dataset includes approximately 8000 test-day milk yields from 900 cows on five farms in Gloucester, UK, collected over 18 mo from 1997 to 1999. The data were structured to account for repeated measures of test-day yield (1 to 10 per cow) and analyzed to account for this autocorrelation. Factors affecting milk yield included: farm of origin, stage of lactation, parity, and whether a cow ever became lame. In clinically lame cows, milk yield was reduced from up to 4 mo before a case of lameness was diagnosed and treated and for the 5 mo after treatment. The total mean estimated reduction in milk yield per 305-d lactation was approximately 360 kg. We conclude that clinical lameness has a significant impact on milk production. This is important information for assessing the economic impact of clinical lameness and its impact on cow health. It adds weight to the importance of early identification of clinical lameness and the urgency of techniques to improve the definition of this highly subjective diagnosis.

A protocol was developed by consultation with experts on the welfare of cattle to use direct observations of cattle and an examination of farm records to assess welfare. Fifty-three dairy farms in England were visited and assessed during the winter of 2000/01. The findings were compiled and the results of the welfare measurements were examined by 50 experts who indicated at what level they considered that improvement was required. More than 75 per cent of them considered that 32 of the 53 farms needed to take action to reduce the incidence of mastitis, and that at least 42 of the farms needed to take action to reduce the prevalence of lameness, overgrown claws, swollen and ulcerated hocks, and injuries from the environment.

A survey of clinical and subclinical mastitis was carried out on 97 dairy farms in England and Wales, selected at random from members of a national milk recording scheme. The farmers were asked to collect aseptic milk samples from five consecutive cases of clinical mastitis and from five quarters with high somatic cell counts using a defined protocol, and they completed a questionnaire that included information on the cows sampled, the herd and the history of mastitis in the herd. The samples were collected throughout the year. The mean incidence of clinical mastitis was 47 cases per 100 cows per year (estimated from historic farm records) and 71 cases per 100 cows per year (estimated from the samples collected). Streptococcus uberis and Escherichia coli were isolated in pure culture from 23.5 per cent and 19.8 per cent, respectively, of the clinical samples; 26.5 per cent of the clinical samples produced no growth. The most common isolates from the samples with high cell counts were coagulase-negative staphylococci (15 per cent), S uberis (14 per cent) and Corynebacterium species (10 per cent). Staphylococcus aureus and coagulase-positive staphylococci together accounted for 10 per cent of the samples with high somatic cell counts; 39 per cent produced no bacterial growth.

Broiler (meat) chickens have been subjected to intense genetic selection. In the past 50 years, broiler growth rates have increased by over 300% (from 25 g per day to 100 g per day). There is growing societal concern that many broiler chickens have impaired locomotion or are even unable to walk. Here we present the results of a comprehensive survey of commercial flocks which quantifies the risk factors for poor locomotion in broiler chickens. We assessed the walking ability of 51,000 birds, representing 4.8 million birds within 176 flocks. We also obtained information on approximately 150 different management factors associated with each flock. At a mean age of 40 days, over 27.6% of birds in our study showed poor locomotion and 3.3% were almost unable to walk. The high prevalence of poor locomotion occurred despite culling policies designed to remove severely lame birds from flocks. We show that the primary risk factors associated with impaired locomotion and poor leg health are those specifically associated with rate of growth. Factors significantly associated with high gait score included the age of the bird (older birds), visit (second visit to same flock), bird genotype, not feeding whole wheat, a shorter dark period during the day, higher stocking density at the time of assessment, no use of antibiotic, and the use of intact feed pellets. The welfare implications are profound. Worldwide approximately 2×1010 broilers are reared within similar husbandry systems. We identify a range of management factors that could be altered to reduce leg health problems, but implementation of these changes would be likely to reduce growth rate and production. A debate on the sustainability of current practice in the production of this important food source is required.