Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.

Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.

Impact statement

Bacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being.

Data summary

The genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. ' frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 ( B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at doi.org/10.25451/flinders.21946034.

The human gut virome: composition, colonization, interactions, and impacts on human health

The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.

Pre-employment health assessments for food handlers: a survey of occupational physicians in the food industry

The format of pre-employment health screens within the food industry varies considerably. The aim of this study was to produce a consensus on the content of a screen that will enable employees to handle food with minimum risk to the product and employee. A questionnaire was sent to the 63 members of the Food Industry Medical Association, of whom 45 (71%) responded. As a minimum, a questionnaire completed by the applicant is thought to be sufficient. Applicants reporting health problems need to be assessed by a health professional.

The development of circadian rhythms in a human infant

STUDY OBJECTIVES

This study examines the ontogeny and interaction of circadian rhythms of sleep, wake, temperature, melatonin, and feeding in the human newborn, and the influence of photic and non-photic factors on the initiation of entrainment.

DESIGN

An infant's sleep-wake state, temperature, and salivary melatonin were monitored from birth to 6 months. Temperature was obtained every hour, and the infant's sleep/eating onset/termination were observed continuously and recorded until day 182. Salivary melatonin was obtained weekly for a 24-hour period, starting at week 3.

SETTING

The infant slept in his parents' bedroom. All household members awakened, retired, and ate meals according to a fixed schedule during the study, while the infant ate, slept, and woke on demand.

PARTICIPANTS

A healthy male infant was the subject. Biological parents gathered data continuously for six months.

INTERVENTIONS

The infant's schedule was on-demand; the household's was fixed. Illumination was restricted to sunlight.

MEASUREMENTS AND RESULTS

The circadian rhythm of temperature appeared first, soon after birth, and became statistically significant within one week. The wake circadian rhythm appeared second, attaining significance at day 45; approximately the same time that increased melatonin concentration began to occur at sunset. The sleep circadian rhythm appeared last, attaining significance after day 56. Ninety to 120 minute zones of sustained wakefulness first appeared in the second month of life subsequent to awakening and prior to sleep onset. The infant's nocturnal sleep-onset was coupled to sunset before day 60 and subsequently to family bedtime, giving evidence of initial photic entrainment followed by social entrainment.

CONCLUSIONS

Circadian rhythms appeared much more rapidly in this infant than previously reported; their rapid appearance was probably facilitated by maximal exposure to sunlight, and regular social cues. These lighting conditions replicate universal infant experience prior to the invention of artificial light.

Oilseed rape and bronchial reactivity

OBJECTIVES

To investigate atopy and changes in symptoms, peak flow rate, and bronchial reactivity in people complaining of symptoms during the oilseed rape flowering season.

METHODS

37 people who had given positive answers to questions about the presence of symptoms in relation to the flowering season of oilseed rape and 24 controls with no such symptoms were studied, although not all took part in all parts of the study. All had been previously identified in a cross sectional survey of a random sample of a rural population. Atopy was assessed by means of skin prick tests, total immunoglobulin E (IgE), and radioallergosorbent test (RAST) assays. Bronchial reactivity (PC20) was measured by histamine challenge. Total IgE and bronchial reactivity were measured both before and during the oilseed rape flowering season. Day to day changes were monitored by subjects who kept a record of their symptoms and peak flow morning and evening, starting before the flowering season and continuing during it and into the grass pollen season.

RESULTS

Only two cases, of 23 tested, showed evidence of allergy to oilseed rape and only 10 of 23 tested, including these two, were atopic. Eye, nasal, and headache symptoms increased in the season in cases, which validated the questionnaire used in the previous cross sectional survey. 12 of 16 cases tested and seven of 15 controls showed a seasonal fall in PC20; the fall in the cases was significantly greater than in the controls. Peak flow charts showed no evidence of fall or of increased variability during the season.

CONCLUSIONS

People who complained of symptoms in relation to the flowering of oilseed rape were rarely allergic to the plant and fewer than half were atopic. Nevertheless, they usually showed increased bronchial reactivity during the season, which may have been due in some cases to other allergens but in others to non-specific irritant effects of the air. Whether these are due to chemicals released by the crop, to rising summer ozone levels, or to other factors remains unclear.

Oilseed rape and seasonal symptoms: epidemiological and environmental studies

BACKGROUND

There is widespread concern that the cultivation of oilseed rape leads to seasonal epidemics of respiratory symptoms in populations living in the neighbourhood, and it has been suggested that the plant is a potent allergen. A study was therefore undertaken to determine the prevalence of seasonal symptoms in rural populations close to and far from areas of oilseed rape cultivation, and to measure the levels of allergen and other potentially harmful substances released by the crop.

METHODS

Random samples of 1000 adults from the general practice populations of two villages surrounded by oilseed rape fields, and 1000 adults from one village far from such cultivation, were taken. The subjects completed a previously validated questionnaire on respiratory and other symptoms, including questions on symptom seasonality, occupation, and smoking habits. Pollen and fungal spore counts were made around fields of oilseed rape and in the villages. The chemicals released by oilseed rape were measured in the field.

RESULTS

Overall, 86.8% of the subjects completed the questionnaires and the populations of the two samples were generally comparable. Spring and summer exacerbations of symptoms occurred equally in the two areas in approximately 25% of the population. There were small but significant excesses of cough, wheeze, and headaches in spring in the oilseed rape area (2.3% v 1.1%, 6.8% v 4.6%, and 4.8% v 2.8%, respectively), and cough, wheeze, and itchy skin were more prevalent in smokers. Counts of oilseed rape pollen were generally low except adjacent to fields, and counts of fungal spores were mostly higher in the rape than the non-rape areas. Oilseed rape was shown to give off terpenes and these were detected close to fields.

CONCLUSIONS

While it is likely that a proportion of the spring symptoms occurring in people living in close proximity to oilseed rape is caused by the plant, the excess of such symptoms is small. This, together with the low levels of pollen in the area, suggests that allergy to oilseed rape pollen is uncommon. The general prevalence of seasonal symptoms in rural areas is of interest, and a proportion of these cases is likely to be caused by factors other than allergy. Release of chemicals by plants and natural rises in summer ozone levels may be contributors.

Occupational accidents presenting to the accident and emergency department

A prospective survey of patients attending the major Accident and Emergency Department in Aberdeen was undertaken. This department serves a population of 500,000 and sees some 50% of all accidents in the region. All work-related injuries were identified and information relating to the circumstances of the accident, injury sustained, and treatment required was sought. Work-related injuries accounted for 16.5% of new patients attending the department. The commonest injury type was a laceration to a finger. Three hundred and eighty diagnostic X-rays were undertaken and a total of 910 treatments were required over a 27-day period. On an annual basis, it is estimated that some 5100 radiographs and 12,300 medical treatments would be required for work-related accidents. It is estimated that 30% of injuries to the hands and feet would have been prevented by the wearing of appropriate personal protective equipment. The majority of workplace accidents were correctly referred to A&E and any efforts to reduce this workload must concentrate on preventive measures in the workplace. This paper suggests that documenting work-related accidents and determining targets for preventive action would reduce the number of attendances at A&E units with a potential significant saving for industry and the National Health Service.

Identification of coagulase-negative staphylococci by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and rRNA restriction patterns

A total of 1,417 staphylococcal and micrococcal strains were collected from the beards and scalps of 10 subjects over a period of 8 months. Sixteen strains identified as Staphylococcus epidermidis with an API system had distinctive yellow colonies on nutrient agar plates and sodium dodecyl sulfate-polyacrylamide gel electrophoresis whole-cell polypeptide profiles similar to those of Staphylococcus capitis; this identification was confirmed by analysis of rRNA gene restriction patterns.

Lung abscess: CT-guided drainage

Lung abscesses were drained by means of catheters guided by computed tomography (CT) in 19 patients who still had sepsis despite standard medical therapy; all patients had received antibiotics for at least 5 days, and 11 of the 19 patients had undergone bronchoscopy. The abscess was cured (by clinical and radiographic criteria) in all 19 patients (100%), and surgery was avoided in 16 of the 19 patients (84%). Three patients underwent surgery for removal of organized tissue or decortication after the lung abscess was evacuated. Complications included a hemothorax that required a chest tube in one patient and three minor complications (a clogged catheter in two patients and transient elevation of intracerebral pressure in one patient). The hemothorax occurred in one of two patients in whom the catheter traversed normal lung. The percutaneous drainage catheters traversed juxtaposed abnormal pleura on route to the abscess in 17 of the patients. CT-guided drainage of lung abscess is an effective method to treat lung abscesses that are refractory to conventional therapy; the procedure should obviate major operation in most patients. A catheter route through abscess-pleural syndesis is preferable, and CT is useful for planning this route.

Accidents in the workplace

A prospective survey of patients attending the central Accident and Emergency Department and Eye Casualty Department in Aberdeen was made to determine the contribution of accidents at work to the workload of the departments and to estimate risks of injury in different industrial sectors. Work-related injuries accounted for 16.5 per cent of new patients attending the general accident department and 21.7 per cent of those attending eye casualty. Analysis by industrial sector led to estimates that almost one in 10 workers employed in manufacturing industries and in agriculture/forestry/fishing will attend casualty in the course of a year for a work-related injury. The relatively low-risk service sector, because of the large numbers of people employed, contributed the greatest number of individuals with work-related injuries. Two industries had very high rates of specific and preventable injuries--food and fish processing with an estimated 17 knife lacerations per 1000 per annum and mechanical engineering with 60 eye injuries per 1000 per annum. We give reasons for believing that our estimates of risk in the different industrial sectors are conservative.

Bacteriological examination of the water supply on an Antarctic base

Faraday Base represents a small isolated community producing its own domestic water by desalination of sea water. During the Antarctic winter of 1986 (April to October), regular bacteriological examination of the water supply and surrounding sea took place. Samples were collected and examined every 2 weeks by the methods described in the Department of Health and Social Security Report No. 71, on the Bacteriological Examination of Drinking Water Supplies (DHSS, 1982), for membrane filtration and colony counting. The results of these examinations are presented in this paper. The results obtained suggest that water of good bacteriological quality was produced by the desalination plant, but some samples from the distribution system contained coliforms or presumptive Escherichia coli in small numbers. The possible reasons for this low-level contamination are discussed. No cases of gastroenteritis occurred on the base during this time.

Plasma concentrations of the natural anticoagulants protein C and protein S in patients with proteinuria

We measured the plasma concentrations of the natural anticoagulant protein C and its cofactor protein S in 17 patients with severe proteinuria. In addition, prothrombin and antithrombin III levels were measured in the same group of patients. These results were compared with results obtained in 26 healthy controls and a group of 14 patients with chronic renal insufficiency (CRI) but minimal proteinuria. Protein C, protein S, and prothrombin levels were not significantly different between healthy controls and patients with CRI. However, protein C, protein S, and prothrombin levels were significantly elevated in 71%, 82%, and 76%, respectively, of patients with proteinuria. Antithrombin III levels were decreased in three of these 17 patients with proteinuria. Plasma concentrations of protein C, protein S, and prothrombin correlated significantly with each other and were inversely correlated with serum albumin concentrations. In three patients, high protein C, protein S, and prothrombin levels returned to normal during remission of the proteinuric state. Proteins C and S were not detectable in the urine of two patients with high-grade proteinuria. Thus, the plasma levels of the vitamin K-dependent, natural anticoagulant protein C and its cofactor protein S are increased in patients with proteinuria. The elevated plasma levels of other vitamin K-dependent proteins, such as prothrombin, suggest a generalized elevation in vitamin K-dependent protein synthesis in patients with proteinuria.

Response of plasma beta-endorphins to transcutaneous electrical nerve stimulation in healthy subjects

A study of 31 healthy volunteers was done to test the hypothesis that analgesia produced by low frequency/high intensity (LoF/Hil) transcutaneous electrical nerve stimulation (TENS) is mediated by release of beta-endorphin (beta-E). After randomization, Group 1 (n = 10) received no stimulation (placebo); Group 2 (n = 9) received 30 minutes of high frequency/low intensity (HiF/Lol) TENS; and Group 3 (n = 12) received 30 minutes of low frequency/high density (LoF/Hil) TENS. Blood pressure, pulse, plasma beta-E levels, and evoked potential response were measured before and after treatment. Mean plasma beta-E increased with treatment in Groups 2 and 3 and fell in Group 1, but the difference between the groups was not statistically significant. Sixty-seven percent of Groups 2 and 3 showed an increase in plasma beta-E levels compared with 30 percent in Group 1 (two-sample test of proportions, p less than .05). Evoked potential response, a measure of pain threshold, varied directly with plasma beta-E level independent of the type of treatment applied. This study did not demonstrate a difference between the effects of HiF/Lol versus Lof/Hil TENS on plasma beta-E in healthy subjects.