The effect of the probiotic consortia on SARS-CoV-2 infection in ferrets and on human immune cell response in vitro.

Probiotics have been suggested as one solution to counter detrimental health effects by SARS-CoV-2; however, data so far is scarce. We tested the effect of two probiotic consortia, OL-1 and OL-2, against SARS-CoV-2 in ferrets and assessed their effect on cytokine production and transcriptome in a human monocyte-derived macrophage (Mf) and dendritic cell (DC) model. The results showed that the consortia significantly reduced the viral load, modulated immune response, and regulated viral receptor expression in ferrets compared to placebo. In the human Mf and DC model, OL-1 and OL-2-induced cytokine production and genes related to SARS-CoV-2 antiviral immunity. The study results indicate that probiotic stimulation of the ferret immune system leads to improved antiviral immunity against SARS-COV-2, and the genes and cytokines associated with anti-SARS-CoV-2 immunity are stimulated in human immune cells in vitro. The effect of the consortia against SARS-CoV-2 warrants further investigations in human clinical trials.

Epigenetics: A New Frontier in Probiotic Research.

Research into the benefits of probiotics has progressed beyond interventional studies to identifying the underlying molecular mechanisms. Health-promoting effector molecules produced by probiotics are well documented and have been linked to specific genes and even individual nucleotides. However, the factors controlling the expression of these molecules are poorly understood and we argue that epigenetic influences likely play an important role in mediating the health-promoting attributes of probiotics. Here, we review established epigenetic regulation of important microbial genetic systems involved in health promotion, safety, and industrialization to provide evidence that the same regulation occurs in probiotic organisms. We advocate for studies combining genomic and meta-epigenomic data to better understand the mode of action of probiotics, their associated microbiomes, and their effects on consumers.

Draft Genome Sequence of Sulfitobacter sp. CB2047, a Member of the Roseobacter Clade of Marine Bacteria, Isolated from an Emiliania huxleyi Bloom.

We announce the draft genome sequence of Sulfitobacter sp. strain CB2047, a marine bacterium of the Roseobacter clade, isolated from a phytoplankton bloom. The genome encodes pathways for the catabolism of aromatic compounds as well as transformations of carbon monoxide and sulfur species. The strain also encodes a prophage as well as the gene transfer agent (GTA), both of which are prevalent among members of the Rhodobacterales order.

Genome Sequences of Two Temperate Phages, ΦCB2047-A and ΦCB2047-C, Infecting Sulfitobacter sp. Strain 2047.

We announce the complete genome sequences of two temperate Podoviridae, Sulfitobacter phages ΦCB2047-A and ΦCB2047-C, which infect Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. This is the first report of temperate podophage infecting members of the Sulfitobacter genus of the Roseobacter clade.

Genome Sequence of the Sulfitobacter sp. Strain 2047-Infecting Lytic Phage {Phi}CB2047-B.

We announce the complete genome sequence of a lytic podovirus, ΦCB2047-B, which infects the bacterium Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. Genome analysis revealed ΦCB2047-B to be an N4-like phage, with its genome having high nucleotide similarity to other N4-like roseophage genomes.

Marivita roseacus sp. nov., of the family Rhodobacteraceae, isolated from a temperate estuary and an emended description of the genus Marivita.

A gram-negative, non-motile, pigmented, rod-shaped and strictly aerobic bacterium (CB1052(T)) was isolated from a temperate estuary. On the basis of 16S rRNA gene sequence similarity, strain CB1052(T) belongs to the α-3 subclass of the Proteobacteria, within the family Rhodobacteraceae, having the highest similarity to members of the genus Marivita (97.8%) of the Roseobacter lineage. Pylogenetic analysis showed CB1052(T) to be a distinct sister clade to M. litorea and M. cryptomonadis and DNA-DNA relatedness was quite low amongst the strains (< 35%). Strain CB1052(T) cells are non-motile and display a needle-like filamentous form, where individual cells can become quite elongated (up to 15 µm). Similar to M. litorea and M. cryptomonadis, CB1052(T) harbors aerobic anoxygenic photosynthesis genes. However, in contrast to other described Marivita species, strain CB1052(T) actively produces bacteriochlorophyll a. Further physiological features, including antibiotic sensitivities, differentiate strain CB1052(T) from the other members of the genus. Therefore, strain CB1052(T) is considered to represent a novel species of the genus Marivita, for which the name Marivita roseacus sp. nov. is proposed, with the type strain CB1052(T) (=DSM 23118(T) =ATCC BAA 1914(T)).

A protocol for enumeration of aquatic viruses by epifluorescence microscopy using Anodisc™ 13 membranes.

BACKGROUND: Epifluorescence microscopy is a common method used to enumerate virus-like particles (VLP) from environmental samples and relies on the use of filter membranes with pore sizes < 0.02 µm; the most commonly used protocols employ 25 mm Anodisc™ membranes with a built-in support ring. Other filters with small pore sizes exist, including the 13 mm Anodisc™ membranes without a support ring. However, the use of these membranes for viral enumeration has not been previously reported. RESULTS: Here we describe a modified protocol for 13 mm Anodisc membranes that uses a custom filter holder that can be readily constructed in individual investigators' laboratories from commercially available Swinnex® filter holders. We compared VLP concentrations obtained from phage lysates and seawater samples using both Anodisc membranes, as well as Nuclepore™ small pore-size membranes (0.015 or 0.030 µm). The 13 mm Anodisc membranes gave comparable estimates of VLP abundance to those obtained with the 25 mm Anodisc membranes when similar staining methods were employed. Both Nuclepore membranes typically gave an order of magnitude lower VLP abundance values for environmental samples. CONCLUSIONS: The 13 mm Anodisc membranes are less costly and require smaller sample volumes than their 25 mm counterpart making them ideal for large-scale studies and sample replication. This method increases the options of reliable approaches available for quantifying VLP from environmental samples.

Estimating virus production rates in aquatic systems.

Viruses are pervasive components of marine and freshwater systems, and are known to be significant agents of microbial mortality. Developing quantitative estimates of this process is critical as we can then develop better models of microbial community structure and function as well as advance our understanding of how viruses work to alter aquatic biogeochemical cycles. The virus reduction technique allows researchers to estimate the rate at which virus particles are released from the endemic microbial community. In brief, the abundance of free (extracellular) viruses is reduced in a sample while the microbial community is maintained at near ambient concentration. The microbial community is then incubated in the absence of free viruses and the rate at which viruses re-occur in the sample (through the lysis of already infected members of the community) can be quantified by epifluorescence microscopy or, in the case of specific viruses, quantitative PCR. These rates can then be used to estimate the rate of microbial mortality due to virus-mediated cell lysis.

Arsenite-dependent photoautotrophy by an Ectothiorhodospira-dominated consortium.

Over the past decade numerous lineages of bacteria have been shown to obtain energy for growth through redox transformations of arsenic. However, phototrophic growth using reduced arsenic as an electron donor has not been described. Here we report the light-dependent oxidation of arsenite to arsenate, coupled with autotrophic growth, by an Ectothiorhodospira-dominated consortium of bacteria from alkaline, hypersaline Mono Lake, California. Pure cultures of the Mono Lake Ectothiorhodospira were not capable of phototrophic arsenite oxidation under the culture conditions tested. Electron micrographs of the culture showed a close association between consortia members, although the specific contribution of the individual bacteria is currently unknown. This report extends the list of compounds known to support anoxygenic photosynthesis and documents a previously unknown pathway in arsenic geochemistry.

Relevance of ammonium oxidation within biological soil crust communities.

Thin, vertically structured topsoil communities that become ecologically important in arid regions (biological soil crusts or BSCs) are responsible for much of the nitrogen inputs into pristine arid lands. We studied N(2) fixation and ammonium oxidation (AO) at subcentimetre resolution within BSCs from the Colorado Plateau. Pools of dissolved porewater nitrate/nitrite, ammonium and organic nitrogen in wetted BSCs were high in comparison with those typical of aridosoils. They remained stable during incubations, indicating that input and output processes were of similar magnitude. Areal N(2) fixation rates (6.5-48 micromol C(2)H(2) m(-2) h(-1)) were high, the vertical distribution of N(2) fixation peaking close to the surface if populations of heterocystous cyanobacteria were present, but in the subsurface if they were absent. Areal AO rates (19-46 micromol N m(-2) h(-1)) were commensurate with N(2) fixation inputs. When considering oxygen availability, AO activity invariably peaked 2-3 mm deep and was limited by oxygen (not ammonium) supply. Most probable number (MPN)-enumerated ammonia-oxidizing bacteria (6.7-7.9 x 10(3) cells g(-1) on average) clearly peaked at 2-3 mm depth. Thus, AO (hence nitrification) is a spatially restricted but important process in the nitrogen cycling of BSC, turning much of the biologically fixed nitrogen into oxidized forms, the fate of which remains to be determined.