Background
Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population‐based studies of cattle have investigated how the microbiota is impacted during diarrhea.
...Objectives
To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.
Methods
Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age‐matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high‐throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).
Results
Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.
Clinical Relevance
The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.
Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the ...tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.
Non‐melanoma skin cancers commonly contain Human Papillomavirus (HPV), but the types found have varied depending on the polymerase chain reaction (PCR) primer systems used. Whole genome amplified DNA ...(not amplified by any specific PCR primers) from 91 skin lesions 41 squamous cell skin carcinomas (SCCs), 8 keratoacanthomas, 22 actinic keratoses, 3 basal cell carcinomas and 17 SCCs in situ were sequenced. All samples were sequenced both at 160 Mb and 1.8 Gb sequencing depth per sample. The sequences from 10 different HPVs in 47/91 specimens were found. Sequences represented four established HPV types (HPV types 16, 22, 120, 124), two previously known putative types (present in GenBank) and four previously unknown HPV sequences (new putative types). The most commonly detected virus was cloned, sequenced and designated as HPV197. Type‐specific real‐time PCR detected HPV197 in 34/91 specimens. For comparison, a pool of the same samples after general primer PCR amplification was also sequenced. This revealed 40 different HPVs, but only two HPV types were detected both with sequencing without prior PCR and with sequencing PCR amplicons, suggesting that sequencing without prior PCR gives a more unbiased representation of the HPVs present. In summary, it was found that HPV can be sequenced from most skin disease specimens and HPV197 appeared to be the most commonly present virus.
What's new?
Some skin cancers such as squamous cell carcinomas occur more often in immune compromised individuals, pointing to an infectious agent as cause. In an unbiased approach the authors used next‐generation sequencing to examine 91 non‐melanoma skin cancer lesions. Most skin lesions contained Human Papilloma Virus (HPV). The authors cloned and sequenced a new type, HPV type 197, present in 34 of the 91 skin lesions. HPV197 has only 75% similarity with the most closely related known HPV (HPV178), suggesting a possible new agent involved in the carcinogenesis of non‐melanoma skin lesions.
•Bioremediation of PAHs is limited by a poor predictability of end points.•A wide range of innovations have been achieved in recent years addressing this issue.•Innovations are related to ...surfactants, chemotactic inoculants, plants and electrokinetics.•These strategies can be integrated into practical remediation protocols.
The current poor predictability of end points associated with the bioremediation of polycyclic aromatic hydrocarbons (PAHs) is a large limitation when evaluating its viability for treating contaminated soils and sediments. However, we have seen a wide range of innovations in recent years, such as an the improved use of surfactants, the chemotactic mobilization of bacterial inoculants, the selective biostimulation at pollutant interfaces, rhizoremediation and electrobioremediation, which increase the bioavailability of PAHs but do not necessarily increase the risk to the environment. The integration of these strategies into practical remediation protocols would be beneficial to the bioremediation industry, as well as improve the quality of the environment.
•There are marked differences in intestinal microbiota among intestinal compartments of horses.•There was a significant increase in diversity towards the distal gut.•A stable bacterial population was ...observed from the cecum through feces.•Fecal samples may represent changes occurring in the distal compartments of the equine gastrointestinal tract.
The advance of new sequencing technologies has allowed more comprehensive characterization of complex microbial communities, including the ones inhabiting the intestinal tract. The presence of extreme environmental filters, such as low pH, digestive enzymes and anaerobic conditions along the tract, acts on the selection of unique bacteria in each compartment. The intestinal microbiota has an enormous impact on the maintenance of health. However, data about the bacteria present in the different intestinal compartments of horses are sparse. In this study, high throughput sequencing was used to characterize and compare bacterial profiles from different intestinal compartments of 11 horses scheduled for euthanasia for reasons other than gastrointestinal problems.
Marked differences among compartments even at high taxonomic levels were found, with Firmicutes comprising the main bacterial phylum in all compartments. Lactobacillus spp. and Sarcina spp. predominated in the stomach and a marked increase of Streptococcus spp. occurred in the duodenum. Actinobacillus and Clostridium sensu stricto were the most abundant genera in the ileum and ‘5 genus incertae sedis’, a genus from the Subdivision 5 class of the Verrucomicrobia, was the most abundant from the large colon through feces. There was a significant increase in diversity towards the distal gut with similar profiles observed from the cecum through feces at the class level. The bacterial population comprising the equine intestinal tract varies greatly among compartments and fecal samples may be useful as representative of changes occurring in the distal compartments.
We analysed 1040 individual trees, located in 62 plots across the Amazon Basin for leaf mass per unit area (MA), foliar carbon isotopic composition (δ13C) and leaf level concentrations of C, N, P, ...Ca, Mg, K and Al. All trees were identified to the species level with the dataset containing 58 families, 236 genera and 508 species, distributed across a wide range of soil types and precipitation regimes. Some foliar characteristics such as MA, C, N and Mg emerge as highly constrained by the taxonomic affiliation of tree species, but with others such as P, K, Ca and δ13C also strongly influenced by site growing conditions. By removing the environmental contribution to trait variation, we find that intrinsic values of most trait pairs coordinate, although different species (characterised by different trait suites) are found at discrete locations along a common axis of coordination. Species that tend to occupy higher fertility soils are characterised by a lower MA and have a higher intrinsic N, P, K, Mg and δ13C than their lower fertility counterparts. Despite this consistency, different scaling patterns were observed between low and high fertility sites. Inter-relationships are thus substantially modified by growth environment. Analysing the environmental component of trait variation, we found soil fertility to be the most important predictor, influencing all leaf nutrient concentrations and δ13C and reducing MA. Mean annual temperature was negatively associated with leaf level N, P and K concentrations. Total annual precipitation positively influences MA, C and δ13C, but with a negative impact on Mg. These results provide a first basis for understanding the relationship between the physiological functioning and distribution of tree species across Amazonia.
Low birth weight and rapid postnatal weight gain are independent predictors of obesity and diabetes in adult life, yet the molecular events involved in this process remain unknown. In inbred and ...outbred mice, this study examines natural intrauterine growth restriction (IUGR) in relation to body weight, telomere length (TL), glucose tolerance, and growth factor gene (
,
,
,
, and
) mRNA expression levels in the brain, liver, and muscle at 2- and 10 days of age and then at 3- and 9 months of age. At birth, ~15% of the animals showed IUGR, but by 3 and 9 months, half of these animals had regained the same weight as controls without IUGR (recuperated group). At 10 days, there was no difference in TL between animals undergoing IUGR and controls. However, by 3 and 9 months of age, the recuperated animals had shorter TL than the control and IUGR-non recuperated animals and also showed glucose intolerance. Further, compared to controls,
and
growth factor mRNA expression was lower in Day 2-IUGR mice, while
and
mRNA expression was higher in D10-IUGR animals. Moreover, at 3 months of age, only in the recuperated group were brain and liver
,
,
, and
expression levels higher than in the control and IUGR-non-recuperated groups. These data indicate that catch-up growth but not IUGR per se affects TL and glucose tolerance, and suggest a role in this latter process of insulin/insulin-like growth signaling pathway gene expression during early development.
Pneumococcal parapneumonic empyema is an increasingly common complication in children. Conventional microbiological cultures indicate bacterial causes in as few as 8% of cases; therefore, there is a ...vital need for new molecular methods of detection and diagnosis. The development and clinical evaluation of real-time PCR-based assays to detect the pneumococcal capsular wzg gene of all serotypes tested are reported here, and 24 of them have been identified in clinical specimens. Using real-time PCR assays with highly specific TaqMan MGB probes that target DNA sequences within the capsular polysaccharide gene cluster, it was possible to differentiate serotypes 1, 3,5,4, 6A, 6B, 7F/A, 8, 9V/A/N/L, 14, 15B/C, 18C/B, 19A, 19F/B/C, 23F and 23A. These assays showed high sensitivity (five to ten pneumococcal DNA equivalents) and they were validated with 175 clinical isolates of known serotypes. The clinical value of this approach was demonstrated by analysis of 88 culture-negative pleural fluids from children diagnosed with parapneumonic empyema in three Spanish hospitals. Pneumococcal DNA was detected in 87.5% of pleural fluids, and serotypes 1, 7F and 3 were responsible for 34.3%, 16.4% and 11.9%, respectively, of cases of parapneumonic empyema in children. Such molecular methods are critical for the diagnosis of invasive pneumococcal disease and continued epidemiological surveillance in order to monitor serotype vaccine effectiveness.
•On dairy farms, prevalence of calf diarrhoea was linked to antimicrobial drug usage.•Improved disease detection and colostrum management reduced antimicrobial drug use.•Treatment algorithms resulted ...in a reduction in the number of calves treated.•Reduced antimicrobial treatment was not associated with increased calf mortality.
This study evaluated the impact of a multidisciplinary intervention to reduce and refine antimicrobial drug use for treatment of diarrhoea in dairy calves. The intervention consisted of modification of management practices for disease prevention, health evaluation training of farm staff, implementation of an algorithm directed at antimicrobial therapy for diarrhoeic calves, and monthly farm visits. A combination of retrospective (before intervention period BP, 1 year) and prospective (immediately after intervention period AP, 1 year) cohorts were used. Health outcomes measured included incidence of diarrhoea and overall mortality. Antimicrobial treatment rates for diarrhoea and total mass of antimicrobial drugs used at the calf and farm level were also evaluated. Outcomes were assessed using the χ2 or Fisher’s exact test, and odds ratios and 95% confidence intervals (95% CI) were calculated.
Records of 2049 and 2251 calves from 10 farms were available in the BP and AP, respectively. Reduced antimicrobial treatment rates occurred on seven farms (P < 0.01), but not on three farms in the AP. A total of 85% (1303/1573) and 18% (310/1698) of diarrhoeic calves were treated with antimicrobial drugs in the BP and AP (P < 0.001), respectively. There were no differences in the incidence of diarrhoea or mortality between periods. In the AP, the use sulfamethazine and trimethoprim decreased on eight farms, one farm discontinued use of lincomycin and spectinomycin, while two farms discontinued use and one reduced use of cephalosporins. This multidisciplinary approach was effective in reducing antimicrobial drug use for calf diarrhoea on dairy farms without negative impacts on calf health.
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