Slaughterhouse facilities in developing nations: sanitation and hygiene practices, microbial contaminants and sustainable management system.

Poor personal and environmental hygiene and sanitary conditions of abattoirs in developing countries in sub-Saharan Africa have been implicated in the occurrence and spread of foodborne diseases. This focused review aims to evaluate the sanitation and hygiene practices of slaughterhouses in selected sub-Saharan African countries as well as the microbial (bacterial) contaminants associated with these slaughterhouses. Pathogenic microorganisms of public health importance have been associated with these slaughterhouses due to poor hygiene conditions, non-formal occupational health and safety training, and poor knowledge of workers as well as substandard infrastructures and crude tools in these facilities. Put together, these conditions enable the growth, survival, transmission, and proliferation of foodborne pathogens such as bacteria, parasites, and viruses. To address this issue, there is a need to assess the poor environmental and personal hygiene of butchers and other abattoir workers, the inaccessibility of potable water, waste management practices, and the lack of appropriate infrastructure and technology, which have been identified as some of the enabling factors for bacteria, fungi, and viruses. Sustainable strategies should include instituting regulations that are backed by law.

Alterations in energy metabolism, total protein, uric and nucleic acids in African sharptooth catfish (Clarias gariepinus Burchell) exposed to crude oil and fractions.

Water contamination by crude oil is a growing challenge and little is known about the probabilistic and non-probabilistic ecosystem and species consequences. Therefore, research aimed at understanding species survival strategy in crude oil-contaminated environments with focus on cellular metabolic alterations and dynamics is vital. This study assessed the alterations in lactate dehydrogenase (LDH), glucose (GLU), glucose-6-phosphate dehydrogenase (G-6-PDH), total protein (TP), uric and nucleic acids (UA, RNA, and DNA) in the liver, heart, kidney, blood supernatants, and muscle homogenates of African sharptooth catfish ([ASC] Clarias gariepinus) exposed to varying bonny-light crude oil concentrations to understand the underlying cause of their delayed development as well as potential health and wellbeing. Three concentrations (20, 50, and 100 mg/L) of diluted whole bonny-light crude oil (DWC), water-soluble (WSF), and water-insoluble (WIF) fractions of bonny-light crude oil were used to grow ASC for 9 weeks at room temperature. Biochemical assessments revealed significant (at p < 0.05) elevations in heart LDH (48.57 ± 4.67 to 3011.34 ± 4.67 U/L) and blood G-6-PDH activities (54.86 ± 0.00 to 128 ± 18.29 mU/mL), GLU (0.22 ± 0.01 to 0.77 ± 0.01 mg/dL), TP (5.15 ± 0.14 to 22.33 ± 0.21 g/L), UA (0.29 ± 0.05 to 10.05 ± 0.27 mg/dL), as well as liver DNA (0.38 ± 0.02 to 2.33 ± 0.09 µg/mL) and RNA (12.52 ± 0.05 to 30.44 ± 0.02 µg/mL) levels for laboratory-grown ASC in DWC, WSF, WIF, and oil-impacted Ubeji river collected ASC relative to the control. Due to greater levels of cellular metabolic alterations in oil-impacted Ubeji River collected ASC, it is evident that bonny-light contamination levels in the river is greater than 100 mg/L. In conclusion, bonny-light crude oil is toxic to ASC and induces stress response. The ecological changes caused by bonny-light crude oil contamination may ultimately affect niche functioning and the development of organs in ASC.

The place of neglected and underutilized legumes in human nutrition and protein security in Nigeria.

The enormous effects of food insecurity have worsened in Nigeria and are further heightened by internal conflicts combined with ongoing climate change impacts such as drought and floods. Moreover, food availability is affected by economic challenges especially a weakening of foreign exchange and fiscal revenues, which has reduced the rate of food importation and increased local prices. Furthermore, the geometric increase in population especially in the last five decades has placed enormous pressure on the limited food resources, making it more challenging for agricultural and food systems to sustainably meet local food needs. Put together, these indices are contributing significantly to undernourishment. The huge local legume resources if properly harnessed can contribute toward addressing food insecurity. However, most of the legumes are included in the United Nations' Food and Agriculture Organization list of underutilized crops. Also, there is an over-reliance on food high in calorie in Nigeria, which is discouraged by nutritionists worldwide. Plant-based protein from legumes is necessary for effective metabolism and human wellbeing. This work highlights the benefits of the sustainable utilization of neglected and underutilized legume resources in Nigeria. The work discusses potential solutions for food insecurity as well as avenues for improving human nutrition and wellbeing.

Genomic and in vitro properties of the dairy Streptococcus thermophilus SMQ-301 strain against selected pathogens.

Cumulative studies have suggested that probiotic bacterial strains could be an effective alternative in inhibiting conditions caused by foodborne and vaginal pathogens. The use of genomic techniques is becoming highly useful in understanding the potential of these beneficial microorganisms. This study presents some genomic and in vitro properties of the Streptococcus thermophilus SMQ-301 strain against foodborne and vaginal pathogens (Staphylococcus aureus, Escherichia coli, and Gardnerella vaginalis) to validate its use in dairy food formulations. Genomic analyses include bacteriocin production, stress response systems, antioxidant capability, and RAST-based functional annotation. In vitro investigations focused on the antimicrobial effects of the S. thermophilus SMQ-301 cell-free solution (CFS) against the selected pathogens after enzymatic actions and pH treatments, assessment of cytotoxic effects using murine RAW264.7 cells, and assessment of organic acid production levels using supplementary carbon sources. The results show that the S. thermophilus SMQ-301 genome possesses essential pathways for stress management, antioxidant activities, and bacteriocin production. For the first time, the bacteriocin-producing peptides of S. thermophilus SMQ-301 are reported, which gives an insight into its inhibitory potential. In vitro, the CFS of S. thermophilus SMQ-301 had significant (P < 0.05) antimicrobial effects on the selected pathogens, with S. aureus ATCC25923 being the most resistant. All antimicrobial activities of the CFS against the selected pathogens were eliminated at pH 6.5 and 7.0. S. thermophilus SMQ-301 CFS yielded the highest lactic (25.58 ± 0.24 mg mL-1) and acetic (5.53 ± 0.12 mg mL-1) acid production levels, with 1% fructooligosaccharide (P < 0.05). The S. thermophilus SMQ-301 strain also lowered murine RAW264.7 cell activities from 101.77% (control) to 80.16% (T5 - RAW264.7 cells + 1 × 109 CFU mL-1 cells) (P < 0.05). This study showed that although the S. thermophilus SMQ-301 strain had excellent genomic characteristics, the in vitro effects varied markedly against all three pathogens. In all, the S. thermophilus SMQ-301 strain has promising applications as a potential probiotic in the food and allied industries.

Correction: Suppressive effects of Streptococcus thermophilus KLDS 3.1003 on some foodborne pathogens revealed through in vitro, in vivo and genomic insights.

Correction for 'Suppressive effects of Streptococcus thermophilus KLDS 3.1003 on some foodborne pathogens revealed through in vitro, in vivo and genomic insights' by Smith Etareri Evivie et al., Food Funct., 2020, 11, 6573-6587, DOI: .

Suppressive effects of Streptococcus thermophilus KLDS 3.1003 on some foodborne pathogens revealed through in vitro, in vivo and genomic insights.

Foodborne diseases (FBDs) remain a persistent global challenge and recent research efforts suggest that lactic acid bacteria (LAB) strains can contribute towards their prevention and treatment. This study investigates the genetic properties of Streptococcus thermophilus KLDS 3.1003 as a potential probiotic and health-promoting LAB strain as well as its in vitro and in vivo activities against two foodborne pathogens. In vitro, its antimicrobial activities and tolerance levels in simulated bile salts and acids were determined. The cytotoxic effects of the LAB strain in RAW264.7 cells were also evaluated. For in vivo evaluation, 24 BALB/c mice were orally administered control and trial diets for 14 days. Genomic analyses of this strain's bacteriocin configuration, stress response system and multidrug resistance genes were annotated to validate in vitro and in vivo results. In vitro antimicrobial results show that the cells and CFS of S. thermophilus KLDS 3.1003 could inhibit both pathogens with the former being more effective (P < 0.05). In addition, its cell-free supernatant (CFS) could inhibit the growth of both pathogens, with catalase treatment having the highest effect against it. More so, after 3 h of incubation, survivability levels of S. thermophilus KLDS 3.1003 were significantly high (P < 0.05). LPS-induced RAW264.7 cell activities were also significantly reduced by 108-109 CFU mL-1 of S. thermophilus KLDS. In vivo, significant weight losses were inhibited in the TSTEC group compared to the TSTSA group (P < 0.05). Moreover, pathogen-disrupted blood biochemical parameters like HDL, LDL, TP, TG, AST, ALT and some minerals were restored in the respective prevention groups (TSTEC and TSTSA). Genomic analyses showed that S. thermophilus KLDS 3.1003 has bacteriocin-coding peptides, which accounts for its antimicrobial abilities in vitro and in vivo. S. thermophilus KLDS 3.1003 is also endowed with intact genes for acid tolerance, salt-resistance, cold and heat shock responses and antioxidant activities, which are required to promote activities against the selected foodborne pathogens. This study showed that S. thermophilus KLDS 3.1003 has the genomic capacity to inhibit foodborne pathogens' growth in vitro and in vivo, thus qualifying it as a potential probiotic, antimicrobial and bio-therapeutic candidate.

Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.

The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently "metal-tolerant" community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.

Tropical forest conversion to rubber plantation in southwest China results in lower fungal beta diversity and reduced network complexity.

Despite the extensive, ongoing conversion of tropical forests to rubber plantation, the effects of this land-use change on soil fungal community diversity and composition are still poorly known. We compared a network of sites of tropical forest in southern Yunnan, China, with a network of rubber plantation sites originally derived from this forest. Soil DNA was amplified for ITS2 and sequenced using Illumina MiSeq. We found that there was a major shift in community composition across all phyla, including a large reduction in ectomycorrhizal fungi likely related to the absence of hosts. Conversion from forest to rubber plantation had no effect on total fungal α-diversity, but rubber plantation had lower ß-diversity, resulting in lower overall gamma diversity. Networks based on co-occurrence of operational taxonomic unit in each land-use type showed that network complexity decreased with land-use change from forest to rubber plantation. Further investigation of soil functionality is needed to investigate whether this lower network complexity is related to reduced soil ecosystem resilience.

Changes in soil taxonomic and functional diversity resulting from gamma irradiation.

Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of 60Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAST. We hypothesized that with increasing radiation exposure there would be a decrease in both taxonomic and functional diversity. While bacterial diversity decreased, diversity of fungi and algae unexpectedly increased, perhaps because of release from competition. Despite the decrease in diversity of bacteria and of biota overall, functional gene diversity of algae, bacteria, fungi and total biota increased. Cycles of radiation exposure may increase the range of gene functional strategies viable in soil, a novel ecological example of the effects of stressors or disturbance events promoting some aspects of diversity. Moreover, repeated density-independent population crashes followed by population expansion may allow lottery effects, promoting coexistence. Radiation exposure produced large overall changes in community composition. Our study suggests several potential novel radiation-tolerant groups: in addition to Deinococcus-Thermus, which reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.

Community Ecology of Deinococcus in Irradiated Soil.

Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.

Fungal Elevational Rapoport pattern from a High Mountain in Japan.

Little is known of how fungal distribution ranges vary with elevation. We studied fungal diversity and community composition from 740 to 2940 m above sea level on Mt. Norikura, Japan, sequencing the ITS2 region. There was a clear trend, repeated across each of the fungal phyla (Basidiomycota, Ascomycota, Zygomycota, Chytridomycota and Glomeromycota), and across the whole fungal community combined, towards an increased elevational range of higher elevation OTUs, conforming to the elevational Rapoport pattern. It appears that fungi from higher elevation environments are more generalized ecologically, at least in terms of climate-related gradients. These findings add to the picture from latitudinal studies of fungal ranges, which also suggest that the classic Rapoport Rule (broader ranges at higher latitudes) applies on a geographical scale. However, there was no mid-elevation maximum in diversity in any of the phyla studied, and different diversity trends for the different phyla, when different diversity indices were used. In terms of functional guilds, on Norikura there were trends towards increased saprotrophism (Zygomycota), symbiotrophism (Basidiomycota), symbiotrophism and saprotrophism (Ascomycota) and pathotrophism (Chytridiomycota) with elevation. The causes of each of these trends require further investigation from an ecological and evolutionary viewpoint.