Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in Ferrets

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1. 

   ScreenIT

   Aug 4, 2021

   SciScore for 10.1101/2021.07.23.453521: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IACUC: The study was performed under American Association for Laboratory Animal Science (IACUC) protocol #20-031 RT-qPCR SARS-CoV-2 Titers: The concentration of virus in nasal washes from study days D1, D3, D5, D7, D9, and D10 was determined by RT-qPCR assay. IRB: The use of human blood was approved by the Ethics Committee of the Hospital District of Helsinki and Uusimaa, Finland (216/13/03/00/2016)
   Sex as a biological variable	All the strains are owned by and were manufactured along with placebo by IFF (Madison, Wisconsin, USA) Ferret studies: Outbred male ferrets
   Randomization	Ferrets were randomly assigned to the different experimental groups.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell…

   SciScore for 10.1101/2021.07.23.453521: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IACUC: The study was performed under American Association for Laboratory Animal Science (IACUC) protocol #20-031 RT-qPCR SARS-CoV-2 Titers: The concentration of virus in nasal washes from study days D1, D3, D5, D7, D9, and D10 was determined by RT-qPCR assay. IRB: The use of human blood was approved by the Ethics Committee of the Hospital District of Helsinki and Uusimaa, Finland (216/13/03/00/2016)
   Sex as a biological variable	All the strains are owned by and were manufactured along with placebo by IFF (Madison, Wisconsin, USA) Ferret studies: Outbred male ferrets
   Randomization	Ferrets were randomly assigned to the different experimental groups.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   To detect the ACE2 by immunohistochemistry, Goat Anti-ACE2 antibody (R&D, Cat#: AF933, Lot#: HOK0620051) was used as the primary antibody.	Anti-ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Bifidobacterium animalis subsp. lactis Bl-04, American Type Culture Collection (ATCC) Safe Deposit (SD)5219, DGCC2908, Lacticaseibacillus paracasei subsp. paracasei Lpc-37, SD5275, ATCC PTA-4798, Lacticaseibacillus rhamnosus Lr-32, SD5217, and Ligilactobacillus salivarius Ls-33, SD5208, and for OL-2: Bifidobacterium animalis subsp. lactis Bi-07, SD5220, DGCC 2907, Lactobacillus acidophilus NCFM, SD5221, ATCC 700396, Limosilactobacillus fermentum SBS-1, DGCC1925, Lactococcus lactis subsp. lactis Ll-23, DGCC8656, Streptococcus thermophilus subsp. thermophilus St-21, SD5207.	SD5275 suggested: None
   Recombinant DNA
   Sentences	Resources
   PBMCs without stimulation were used as a control, dimethyl sulfoxide (DMSO), a carrier for the TLR-ligands, were used as a control for pIC+R848 containing treatments.	pIC+R848 suggested: None
   Software and Algorithms
   Sentences	Resources
   Cq value in each well was also automatically calculated by the Maestro 1.1 software based on the threshold baseline.	Maestro suggested: (Maestro, RRID:SCR_016748)
   Data generated by the software were exported to a Microsoft Excel (Microsoft Corporation; Redmond, WA) spreadsheet for data processing.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137)
   Slides were viewed and digitized pictures were taken by Olympus VS120 scanner and analyzed by a senior Pathologist using Olyvia 3.2 software (Olympus Corporation, Tokyo, Japan).	Olyvia suggested: (OlyVIA , RRID:SCR_016167)
   Results were analyzed with CiraSoft software (Quanterix).	CiraSoft suggested: None
   The reads were quality filtered, trimmed and demultiplexed and aligned to the BioSpyder Human Whole Transcriptome v2.0 annotated reference using Salmon (v1.1.0)(Patro et al., 2017).	Salmon suggested: (Salmon, RRID:SCR_017036)
   Differential expression analysis was conducted using DESeq2 (v1.26.1)(Love et al., 2014) in R (v 3.6.2).	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   Principal component analysis (PCA) was performed to determine overall relatedness of the samples under the various experimental conditions using ggplot2 (v 3.3.3) (Wickham, 2016)	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Pathway analysis was performed using ROntoTools (v 2.14) (Voichita et al., 2019) with a KEGG pathway (Kanehisa, 2019; Kanehisa et al., 2021; Kanehisa and Goto, 2000) considered significantly changed with a false discovery rate perturbation value of > 0.1.	ROntoTools suggested: None KEGG suggested: (KEGG, RRID:SCR_012773)

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   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.07.23.453521v1 on bioRxiv

   Jul 23, 2021